ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

recreate example logs with new colvars version

Browse Source
This commit is contained in:
Axel Kohlmeyer
2024-08-05 22:12:30 -04:00
parent 04eb6c421d
commit e5957ccc19
23 changed files with 3234 additions and 2736 deletions
Download Patch File Download Diff File Expand all files Collapse all files

629
examples/PACKAGES/colvars/log.27Nov18.peptide-colvars.g++.1
View File

@ -1,629 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 1 by 1 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
group peptide type <= 12
84 atoms in group peptide
group one id 2 4 5 6
4 atoms in group one
group two id 80 82 83 84
4 atoms in group two
group ref id 37
1 atoms in group ref
group colvar union one two ref
9 atoms in group colvar
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
shell "rm -f out*.colvars.*"
fix 2 all colvars peptide.colvars
fix 2a ref setforce 0.0 0.0 0.0
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
thermo_style custom step temp etotal pe ke epair ebond f_2
thermo 10
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 10648 3375
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
colvars: Creating proxy instance
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2018-11-16.
colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars: https://doi.org/10.1080/00268976.2013.813594
colvars: in any publication based on this calculation.
colvars: SMP parallelism is available.
colvars: Using LAMMPS interface, version 2018-08-29.
colvars: ----------------------------------------------------------------------
colvars: Reading new configuration from file "peptide.colvars":
colvars: # smp = on [default]
colvars: # colvarsTrajFrequency = 1
colvars: # colvarsRestartFrequency = 1000
colvars: # scriptedColvarForces = off [default]
colvars: # scriptingAfterBiases = off [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = "one"
colvars: Initializing a new "distance" component.
colvars: # name = "" [default]
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # forceNoPBC = off [default]
colvars: # scalable = on [default]
colvars: Initializing atom group "group1".
colvars: # name = "" [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
colvars: Initializing atom group "group2".
colvars: # name = "" [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
colvars: # oneSiteSystemForce = off [default]
colvars: # oneSiteTotalForce = off [default]
colvars: All components initialized.
colvars: # timeStepFactor = 1 [default]
colvars: # width = 1 [default]
colvars: # lowerBoundary = 0 [default]
colvars: # upperBoundary = 0 [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputTotalForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars: # subtractAppliedForce = off [default]
colvars: # runAve = off [default]
colvars: # corrFunc = off [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = "two"
colvars: Initializing a new "distance" component.
colvars: # name = "" [default]
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # forceNoPBC = off [default]
colvars: # scalable = on [default]
colvars: Initializing atom group "group1".
colvars: # name = "" [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
colvars: Initializing atom group "group2".
colvars: # name = "" [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
colvars: # oneSiteSystemForce = off [default]
colvars: # oneSiteTotalForce = off [default]
colvars: All components initialized.
colvars: # timeStepFactor = 1 [default]
colvars: # width = 1 [default]
colvars: # lowerBoundary = 0 [default]
colvars: # upperBoundary = 0 [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputTotalForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars: # subtractAppliedForce = off [default]
colvars: # runAve = off [default]
colvars: # corrFunc = off [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 2 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "harmonic" instance.
colvars: # name = "h_pot"
colvars: # colvars = { one, two }
colvars: # outputEnergy = off [default]
colvars: # timeStepFactor = 1 [default]
colvars: # writeTISamples = off [default]
colvars: # writeTIPMF = off [default]
colvars: # centers = { 10, 10 }
colvars: # targetCenters = { 10, 10 } [default]
colvars: # outputCenters = off [default]
colvars: # forceConstant = 100
colvars: # targetForceConstant = -1 [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables biases initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Collective variables module (re)initialized.
colvars: ----------------------------------------------------------------------
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
colvars: The restart output state file will be "rest.colvars.state".
colvars: The final output state file will be "out.colvars.state".
colvars: Writing to colvar trajectory file "out.colvars.traj".
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
colvars: Performing analysis.
SHAKE stats (type/ave/delta) on step 0
4 1.111 1.44264e-05
6 0.996998 7.26967e-06
8 1.08 1.32536e-05
10 1.111 1.22749e-05
12 1.08 1.11767e-05
14 0.96 0
18 0.957206 4.37979e-05
31 104.519 0.00396029
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
SHAKE stats (type/ave/delta) on step 100
4 1.11098 8.97155e-05
6 0.996996 1.00568e-05
8 1.08 6.02345e-06
10 1.111 1.84253e-05
12 1.08 7.2713e-06
14 0.959996 0
18 0.957198 3.36079e-05
31 104.52 0.0030599
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
colvars: Saving collective variables state to "out.colvars.state".
Loop time of 2.17304 on 1 procs for 100 steps with 2004 atoms
Performance: 7.952 ns/day, 3.018 hours/ns, 46.018 timesteps/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.5817 | 1.5817 | 1.5817 | 0.0 | 72.79
Bond | 0.0031469 | 0.0031469 | 0.0031469 | 0.0 | 0.14
Kspace | 0.17366 | 0.17366 | 0.17366 | 0.0 | 7.99
Neigh | 0.37354 | 0.37354 | 0.37354 | 0.0 | 17.19
Comm | 0.013652 | 0.013652 | 0.013652 | 0.0 | 0.63
Output | 0.00026059 | 0.00026059 | 0.00026059 | 0.0 | 0.01
Modify | 0.025484 | 0.025484 | 0.025484 | 0.0 | 1.17
Other | | 0.001615 | | | 0.07
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11124 ave 11124 max 11124 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 708237 ave 708237 max 708237 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708237
Ave neighs/atom = 353.412
Ave special neighs/atom = 2.34032
Neighbor list builds = 12
Dangerous builds = 2
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 10648 3375
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
SHAKE stats (type/ave/delta) on step 100
4 1.11098 8.97155e-05
6 0.996996 1.00568e-05
8 1.08 6.02345e-06
10 1.111 1.84253e-05
12 1.08 7.2713e-06
14 0.959996 0
18 0.957198 3.36079e-05
31 104.52 0.0030599
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657
120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812
130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031592
140 253.85111 -5452.1838 -6473.4522 1021.2684 -6609.4826 26.071651 0.30585517
150 261.31816 -5490.4727 -6541.7817 1051.3091 -6646.6076 16.258823 6.9051008
160 255.7352 -5521.5941 -6550.4424 1028.8483 -6658.1373 19.717399 12.339679
170 253.42527 -5540.0942 -6559.6494 1019.5552 -6656.6678 23.293812 10.290217
180 248.51161 -5550.3253 -6550.1124 999.78705 -6661.4235 26.200127 3.4336038
190 250.80862 -5555.2554 -6564.2836 1009.0282 -6666.164 25.53634 3.3494288
SHAKE stats (type/ave/delta) on step 200
4 1.111 1.81266e-06
6 0.997 7.79424e-07
8 1.08 1.08903e-06
10 1.111 2.96503e-07
12 1.08 4.69038e-07
14 0.960001 0
18 0.957201 3.76471e-06
31 104.52 0.000411055
200 251.50475 -5557.4251 -6569.2538 1011.8287 -6674.0845 24.804906 7.1387574
colvars: Saving collective variables state to "out.colvars.state".
Loop time of 2.03298 on 1 procs for 100 steps with 2004 atoms
Performance: 8.500 ns/day, 2.824 hours/ns, 49.189 timesteps/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.5975 | 1.5975 | 1.5975 | 0.0 | 78.58
Bond | 0.0033164 | 0.0033164 | 0.0033164 | 0.0 | 0.16
Kspace | 0.17349 | 0.17349 | 0.17349 | 0.0 | 8.53
Neigh | 0.21971 | 0.21971 | 0.21971 | 0.0 | 10.81
Comm | 0.012045 | 0.012045 | 0.012045 | 0.0 | 0.59
Output | 0.00026226 | 0.00026226 | 0.00026226 | 0.0 | 0.01
Modify | 0.025034 | 0.025034 | 0.025034 | 0.0 | 1.23
Other | | 0.001596 | | | 0.08
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11159 ave 11159 max 11159 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 708083 ave 708083 max 708083 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708083
Ave neighs/atom = 353.335
Ave special neighs/atom = 2.34032
Neighbor list builds = 7
Dangerous builds = 0
fix 2 all colvars peptide.colvars input out.colvars.state output out2
colvars: Resetting the Collective Variables module.
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 10648 3375
colvars: Creating proxy instance
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2018-11-16.
colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars: https://doi.org/10.1080/00268976.2013.813594
colvars: in any publication based on this calculation.
colvars: SMP parallelism is available.
colvars: Using LAMMPS interface, version 2018-08-29.
colvars: ----------------------------------------------------------------------
colvars: Reading new configuration from file "peptide.colvars":
colvars: # smp = on [default]
colvars: # colvarsTrajFrequency = 1
colvars: # colvarsRestartFrequency = 1000
colvars: # scriptedColvarForces = off [default]
colvars: # scriptingAfterBiases = off [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = "one"
colvars: Initializing a new "distance" component.
colvars: # name = "" [default]
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # forceNoPBC = off [default]
colvars: # scalable = on [default]
colvars: Initializing atom group "group1".
colvars: # name = "" [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
colvars: Initializing atom group "group2".
colvars: # name = "" [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
colvars: # oneSiteSystemForce = off [default]
colvars: # oneSiteTotalForce = off [default]
colvars: All components initialized.
colvars: # timeStepFactor = 1 [default]
colvars: # width = 1 [default]
colvars: # lowerBoundary = 0 [default]
colvars: # upperBoundary = 0 [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputTotalForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars: # subtractAppliedForce = off [default]
colvars: # runAve = off [default]
colvars: # corrFunc = off [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = "two"
colvars: Initializing a new "distance" component.
colvars: # name = "" [default]
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # forceNoPBC = off [default]
colvars: # scalable = on [default]
colvars: Initializing atom group "group1".
colvars: # name = "" [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
colvars: Initializing atom group "group2".
colvars: # name = "" [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
colvars: # oneSiteSystemForce = off [default]
colvars: # oneSiteTotalForce = off [default]
colvars: All components initialized.
colvars: # timeStepFactor = 1 [default]
colvars: # width = 1 [default]
colvars: # lowerBoundary = 0 [default]
colvars: # upperBoundary = 0 [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputTotalForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars: # subtractAppliedForce = off [default]
colvars: # runAve = off [default]
colvars: # corrFunc = off [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 2 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "harmonic" instance.
colvars: # name = "h_pot"
colvars: # colvars = { one, two }
colvars: # outputEnergy = off [default]
colvars: # timeStepFactor = 1 [default]
colvars: # writeTISamples = off [default]
colvars: # writeTIPMF = off [default]
colvars: # centers = { 10, 10 }
colvars: # targetCenters = { 10, 10 } [default]
colvars: # outputCenters = off [default]
colvars: # forceConstant = 100
colvars: # targetForceConstant = -1 [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables biases initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Collective variables module (re)initialized.
colvars: ----------------------------------------------------------------------
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
colvars: ----------------------------------------------------------------------
colvars: Restarting from file "out.colvars.state".
colvars: Restarting collective variable "one" from value: 10.0128
colvars: Restarting collective variable "two" from value: 9.62236
colvars: ----------------------------------------------------------------------
colvars: The restart output state file will be "rest.colvars.state".
colvars: The final output state file will be "out2.colvars.state".
colvars: Writing to colvar trajectory file "out2.colvars.traj".
colvars: Setting initial step number from LAMMPS: 200
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
colvars: Performing analysis.
SHAKE stats (type/ave/delta) on step 200
4 1.111 1.81266e-06
6 0.997 7.79424e-07
8 1.08 1.08903e-06
10 1.111 2.96503e-07
12 1.08 4.69038e-07
14 0.960001 0
18 0.957201 3.76471e-06
31 104.52 0.000411055
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
200 251.50475 -5557.4251 -6569.2538 1011.8287 -6674.0845 24.804906 7.1387574
210 253.15303 -5538.5615 -6557.0215 1018.46 -6672.0498 37.67662 0.61219496
220 245.19621 -5522.519 -6508.9679 986.44888 -6628.1899 36.657688 0.04864338
230 258.69884 -5495.7275 -6536.4988 1040.7713 -6658.2885 34.857911 0.22092547
240 260.79635 -5469.8678 -6519.0776 1049.2098 -6624.1801 31.576951 3.7574816
250 269.07527 -5438.3946 -6520.9114 1082.5167 -6616.4383 25.447674 8.6600014
260 266.01049 -5397.3485 -6467.5353 1070.1868 -6580.2897 26.871917 8.3323097
270 272.81313 -5350.882 -6448.4365 1097.5545 -6563.8231 23.114195 10.973131
280 279.42263 -5307.9798 -6432.125 1124.1452 -6557.3367 33.644027 8.5490492
290 286.85172 -5260.841 -6414.8741 1154.0331 -6515.6798 28.574838 5.9100133
SHAKE stats (type/ave/delta) on step 300
4 1.111 1.79792e-05
6 0.997005 1.02512e-05
8 1.08 1.85102e-05
10 1.111 9.98839e-06
12 1.08 8.84111e-06
14 0.960008 0
18 0.957203 1.8445e-05
31 104.52 0.00168383
300 291.52798 -5216.288 -6389.1341 1172.8462 -6503.1276 27.889154 2.2482459
colvars: Saving collective variables state to "out2.colvars.state".
Loop time of 2.07171 on 1 procs for 100 steps with 2004 atoms
Performance: 8.341 ns/day, 2.877 hours/ns, 48.269 timesteps/s
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.6047 | 1.6047 | 1.6047 | 0.0 | 77.46
Bond | 0.0031033 | 0.0031033 | 0.0031033 | 0.0 | 0.15
Kspace | 0.17325 | 0.17325 | 0.17325 | 0.0 | 8.36
Neigh | 0.25117 | 0.25117 | 0.25117 | 0.0 | 12.12
Comm | 0.012173 | 0.012173 | 0.012173 | 0.0 | 0.59
Output | 0.00026488 | 0.00026488 | 0.00026488 | 0.0 | 0.01
Modify | 0.025317 | 0.025317 | 0.025317 | 0.0 | 1.22
Other | | 0.001731 | | | 0.08
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11296 ave 11296 max 11296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 708152 ave 708152 max 708152 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708152
Ave neighs/atom = 353.369
Ave special neighs/atom = 2.34032
Neighbor list builds = 8
Dangerous builds = 0
colvars: Resetting the Collective Variables module.
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:06

629
examples/PACKAGES/colvars/log.27Nov18.peptide-colvars.g++.4
View File

@ -1,629 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 2 by 2 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
group peptide type <= 12
84 atoms in group peptide
group one id 2 4 5 6
4 atoms in group one
group two id 80 82 83 84
4 atoms in group two
group ref id 37
1 atoms in group ref
group colvar union one two ref
9 atoms in group colvar
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
shell "rm -f out*.colvars.*"
fix 2 all colvars peptide.colvars
fix 2a ref setforce 0.0 0.0 0.0
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
thermo_style custom step temp etotal pe ke epair ebond f_2
thermo 10
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 4312 960
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
colvars: Creating proxy instance
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2018-11-16.
colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars: https://doi.org/10.1080/00268976.2013.813594
colvars: in any publication based on this calculation.
colvars: SMP parallelism is available.
colvars: Using LAMMPS interface, version 2018-08-29.
colvars: ----------------------------------------------------------------------
colvars: Reading new configuration from file "peptide.colvars":
colvars: # smp = on [default]
colvars: # colvarsTrajFrequency = 1
colvars: # colvarsRestartFrequency = 1000
colvars: # scriptedColvarForces = off [default]
colvars: # scriptingAfterBiases = off [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = "one"
colvars: Initializing a new "distance" component.
colvars: # name = "" [default]
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # forceNoPBC = off [default]
colvars: # scalable = on [default]
colvars: Initializing atom group "group1".
colvars: # name = "" [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
colvars: Initializing atom group "group2".
colvars: # name = "" [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
colvars: # oneSiteSystemForce = off [default]
colvars: # oneSiteTotalForce = off [default]
colvars: All components initialized.
colvars: # timeStepFactor = 1 [default]
colvars: # width = 1 [default]
colvars: # lowerBoundary = 0 [default]
colvars: # upperBoundary = 0 [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputTotalForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars: # subtractAppliedForce = off [default]
colvars: # runAve = off [default]
colvars: # corrFunc = off [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = "two"
colvars: Initializing a new "distance" component.
colvars: # name = "" [default]
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # forceNoPBC = off [default]
colvars: # scalable = on [default]
colvars: Initializing atom group "group1".
colvars: # name = "" [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
colvars: Initializing atom group "group2".
colvars: # name = "" [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
colvars: # oneSiteSystemForce = off [default]
colvars: # oneSiteTotalForce = off [default]
colvars: All components initialized.
colvars: # timeStepFactor = 1 [default]
colvars: # width = 1 [default]
colvars: # lowerBoundary = 0 [default]
colvars: # upperBoundary = 0 [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputTotalForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars: # subtractAppliedForce = off [default]
colvars: # runAve = off [default]
colvars: # corrFunc = off [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 2 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "harmonic" instance.
colvars: # name = "h_pot"
colvars: # colvars = { one, two }
colvars: # outputEnergy = off [default]
colvars: # timeStepFactor = 1 [default]
colvars: # writeTISamples = off [default]
colvars: # writeTIPMF = off [default]
colvars: # centers = { 10, 10 }
colvars: # targetCenters = { 10, 10 } [default]
colvars: # outputCenters = off [default]
colvars: # forceConstant = 100
colvars: # targetForceConstant = -1 [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables biases initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Collective variables module (re)initialized.
colvars: ----------------------------------------------------------------------
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
colvars: The restart output state file will be "rest.colvars.state".
colvars: The final output state file will be "out.colvars.state".
colvars: Writing to colvar trajectory file "out.colvars.traj".
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
colvars: Performing analysis.
SHAKE stats (type/ave/delta) on step 0
4 1.111 1.44264e-05
6 0.996998 7.26967e-06
8 1.08 1.32536e-05
10 1.111 1.22749e-05
12 1.08 1.11767e-05
14 0.96 0
18 0.957206 4.37979e-05
31 104.519 0.00396029
Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
SHAKE stats (type/ave/delta) on step 100
4 1.11098 8.97155e-05
6 0.996996 1.00568e-05
8 1.08 6.02345e-06
10 1.111 1.84253e-05
12 1.08 7.2713e-06
14 0.959996 0
18 0.957198 3.36079e-05
31 104.52 0.0030599
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
colvars: Saving collective variables state to "out.colvars.state".
Loop time of 0.614168 on 4 procs for 100 steps with 2004 atoms
Performance: 28.136 ns/day, 0.853 hours/ns, 162.822 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.40413 | 0.41468 | 0.42573 | 1.4 | 67.52
Bond | 0.00056815 | 0.0011595 | 0.0017791 | 1.6 | 0.19
Kspace | 0.056367 | 0.066512 | 0.076213 | 3.3 | 10.83
Neigh | 0.095025 | 0.09507 | 0.095124 | 0.0 | 15.48
Comm | 0.015385 | 0.015831 | 0.01623 | 0.2 | 2.58
Output | 0.00026512 | 0.00034493 | 0.00057554 | 0.0 | 0.06
Modify | 0.01938 | 0.019431 | 0.019474 | 0.0 | 3.16
Other | | 0.001141 | | | 0.19
Nlocal: 501 ave 513 max 489 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 6563.25 ave 6596 max 6519 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 177059 ave 181742 max 172942 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 708237
Ave neighs/atom = 353.412
Ave special neighs/atom = 2.34032
Neighbor list builds = 12
Dangerous builds = 2
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 4312 960
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
SHAKE stats (type/ave/delta) on step 100
4 1.11098 8.97155e-05
6 0.996996 1.00568e-05
8 1.08 6.02345e-06
10 1.111 1.84253e-05
12 1.08 7.2713e-06
14 0.959996 0
18 0.957198 3.36079e-05
31 104.52 0.0030599
Per MPI rank memory allocation (min/avg/max) = 15.66 | 15.86 | 16.06 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657
120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812
130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031592
140 253.85111 -5452.1838 -6473.4521 1021.2684 -6609.4826 26.071651 0.30585517
150 261.31816 -5490.4726 -6541.7817 1051.3091 -6646.6075 16.258823 6.9051008
160 255.7352 -5521.5941 -6550.4423 1028.8483 -6658.1373 19.717399 12.339679
170 253.42527 -5540.0941 -6559.6493 1019.5552 -6656.6677 23.293812 10.290217
180 248.51161 -5550.3253 -6550.1124 999.78704 -6661.4235 26.200127 3.4336037
190 250.80862 -5555.2553 -6564.2834 1009.0282 -6666.1638 25.53634 3.3494287
SHAKE stats (type/ave/delta) on step 200
4 1.111 1.81266e-06
6 0.997 7.79424e-07
8 1.08 1.08903e-06
10 1.111 2.96503e-07
12 1.08 4.69038e-07
14 0.960001 0
18 0.957201 3.76471e-06
31 104.52 0.000411055
200 251.50475 -5557.4251 -6569.2539 1011.8288 -6674.0845 24.804905 7.1387572
colvars: Saving collective variables state to "out.colvars.state".
Loop time of 0.569733 on 4 procs for 100 steps with 2004 atoms
Performance: 30.330 ns/day, 0.791 hours/ns, 175.521 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.40512 | 0.41306 | 0.42363 | 1.3 | 72.50
Bond | 0.00061107 | 0.001151 | 0.0017512 | 1.4 | 0.20
Kspace | 0.054393 | 0.063988 | 0.07198 | 3.0 | 11.23
Neigh | 0.056063 | 0.056079 | 0.05609 | 0.0 | 9.84
Comm | 0.013584 | 0.014145 | 0.014649 | 0.3 | 2.48
Output | 0.00026965 | 0.00042897 | 0.00090265 | 0.0 | 0.08
Modify | 0.019253 | 0.019257 | 0.01926 | 0.0 | 3.38
Other | | 0.001623 | | | 0.28
Nlocal: 501 ave 513 max 481 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 6556.5 ave 6608 max 6514 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 177021 ave 182259 max 172089 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 708083
Ave neighs/atom = 353.335
Ave special neighs/atom = 2.34032
Neighbor list builds = 7
Dangerous builds = 0
fix 2 all colvars peptide.colvars input out.colvars.state output out2
colvars: Resetting the Collective Variables module.
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 4312 960
colvars: Creating proxy instance
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2018-11-16.
colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars: https://doi.org/10.1080/00268976.2013.813594
colvars: in any publication based on this calculation.
colvars: SMP parallelism is available.
colvars: Using LAMMPS interface, version 2018-08-29.
colvars: ----------------------------------------------------------------------
colvars: Reading new configuration from file "peptide.colvars":
colvars: # smp = on [default]
colvars: # colvarsTrajFrequency = 1
colvars: # colvarsRestartFrequency = 1000
colvars: # scriptedColvarForces = off [default]
colvars: # scriptingAfterBiases = off [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = "one"
colvars: Initializing a new "distance" component.
colvars: # name = "" [default]
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # forceNoPBC = off [default]
colvars: # scalable = on [default]
colvars: Initializing atom group "group1".
colvars: # name = "" [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
colvars: Initializing atom group "group2".
colvars: # name = "" [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
colvars: # oneSiteSystemForce = off [default]
colvars: # oneSiteTotalForce = off [default]
colvars: All components initialized.
colvars: # timeStepFactor = 1 [default]
colvars: # width = 1 [default]
colvars: # lowerBoundary = 0 [default]
colvars: # upperBoundary = 0 [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputTotalForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars: # subtractAppliedForce = off [default]
colvars: # runAve = off [default]
colvars: # corrFunc = off [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = "two"
colvars: Initializing a new "distance" component.
colvars: # name = "" [default]
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # forceNoPBC = off [default]
colvars: # scalable = on [default]
colvars: Initializing atom group "group1".
colvars: # name = "" [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
colvars: Initializing atom group "group2".
colvars: # name = "" [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
colvars: # oneSiteSystemForce = off [default]
colvars: # oneSiteTotalForce = off [default]
colvars: All components initialized.
colvars: # timeStepFactor = 1 [default]
colvars: # width = 1 [default]
colvars: # lowerBoundary = 0 [default]
colvars: # upperBoundary = 0 [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputTotalForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars: # subtractAppliedForce = off [default]
colvars: # runAve = off [default]
colvars: # corrFunc = off [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 2 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "harmonic" instance.
colvars: # name = "h_pot"
colvars: # colvars = { one, two }
colvars: # outputEnergy = off [default]
colvars: # timeStepFactor = 1 [default]
colvars: # writeTISamples = off [default]
colvars: # writeTIPMF = off [default]
colvars: # centers = { 10, 10 }
colvars: # targetCenters = { 10, 10 } [default]
colvars: # outputCenters = off [default]
colvars: # forceConstant = 100
colvars: # targetForceConstant = -1 [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables biases initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Collective variables module (re)initialized.
colvars: ----------------------------------------------------------------------
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
colvars: ----------------------------------------------------------------------
colvars: Restarting from file "out.colvars.state".
colvars: Restarting collective variable "one" from value: 10.0128
colvars: Restarting collective variable "two" from value: 9.62236
colvars: ----------------------------------------------------------------------
colvars: The restart output state file will be "rest.colvars.state".
colvars: The final output state file will be "out2.colvars.state".
colvars: Writing to colvar trajectory file "out2.colvars.traj".
colvars: Setting initial step number from LAMMPS: 200
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
colvars: Performing analysis.
SHAKE stats (type/ave/delta) on step 200
4 1.111 1.81266e-06
6 0.997 7.79424e-07
8 1.08 1.08903e-06
10 1.111 2.96503e-07
12 1.08 4.69038e-07
14 0.960001 0
18 0.957201 3.76471e-06
31 104.52 0.000411055
Per MPI rank memory allocation (min/avg/max) = 15.66 | 15.86 | 16.06 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
200 251.50475 -5557.4251 -6569.2539 1011.8288 -6674.0845 24.804905 7.1387572
210 253.15304 -5538.5615 -6557.0215 1018.46 -6672.0498 37.676621 0.61219486
220 245.19621 -5522.5189 -6508.9678 986.44888 -6628.1898 36.657688 0.048643368
230 258.69885 -5495.7276 -6536.4989 1040.7713 -6658.2887 34.857911 0.22092541
240 260.79635 -5469.8677 -6519.0775 1049.2098 -6624.18 31.576952 3.7574818
250 269.07527 -5438.3947 -6520.9115 1082.5167 -6616.4384 25.447674 8.6600013
260 266.0105 -5397.3486 -6467.5354 1070.1868 -6580.2898 26.871917 8.3323096
270 272.81314 -5350.8819 -6448.4364 1097.5545 -6563.823 23.114195 10.973131
280 279.42263 -5307.9799 -6432.125 1124.1452 -6557.3367 33.644027 8.5490488
290 286.8517 -5260.8409 -6414.874 1154.0331 -6515.6797 28.574839 5.9100135
SHAKE stats (type/ave/delta) on step 300
4 1.111 1.79792e-05
6 0.997005 1.02512e-05
8 1.08 1.85102e-05
10 1.111 9.98838e-06
12 1.08 8.84113e-06
14 0.960008 0
18 0.957203 1.8445e-05
31 104.52 0.00168382
300 291.52794 -5216.2881 -6389.1342 1172.846 -6503.1276 27.889153 2.248246
colvars: Saving collective variables state to "out2.colvars.state".
Loop time of 0.584942 on 4 procs for 100 steps with 2004 atoms
Performance: 29.541 ns/day, 0.812 hours/ns, 170.957 timesteps/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.41044 | 0.41882 | 0.42773 | 1.1 | 71.60
Bond | 0.00056911 | 0.0011486 | 0.0018017 | 1.4 | 0.20
Kspace | 0.056211 | 0.064277 | 0.072168 | 2.7 | 10.99
Neigh | 0.064606 | 0.064613 | 0.064617 | 0.0 | 11.05
Comm | 0.013311 | 0.013966 | 0.015175 | 0.6 | 2.39
Output | 0.00027871 | 0.00051689 | 0.0012221 | 0.0 | 0.09
Modify | 0.019776 | 0.0199 | 0.020015 | 0.1 | 3.40
Other | | 0.001705 | | | 0.29
Nlocal: 501 ave 513 max 472 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost: 6612.75 ave 6681 max 6561 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Neighs: 177038 ave 180136 max 170218 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Total # of neighbors = 708152
Ave neighs/atom = 353.369
Ave special neighs/atom = 2.34032
Neighbor list builds = 8
Dangerous builds = 0
colvars: Resetting the Collective Variables module.
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:01

260
examples/PACKAGES/colvars/log.27Nov18.peptide-colvars2.g++.1
View File

@ -1,260 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 1 by 1 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
group peptide type <= 12
84 atoms in group peptide
group one id 2 4 5 6
4 atoms in group one
group two id 80 82 83 84
4 atoms in group two
group ref id 37
1 atoms in group ref
group colvar union one two ref
9 atoms in group colvar
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
shell "rm -f peptide2.colvars.*"
fix 2 all colvars peptide.colvars2 output peptide2
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
thermo_style custom step temp etotal pe ke epair ebond f_2
thermo 10
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 10648 3375
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
colvars: Creating proxy instance
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2018-11-16.
colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars: https://doi.org/10.1080/00268976.2013.813594
colvars: in any publication based on this calculation.
colvars: SMP parallelism is available.
colvars: Using LAMMPS interface, version 2018-08-29.
colvars: ----------------------------------------------------------------------
colvars: Reading new configuration from file "peptide.colvars2":
colvars: # smp = on [default]
colvars: # colvarsTrajFrequency = 1
colvars: # colvarsRestartFrequency = 1000
colvars: # scriptedColvarForces = off [default]
colvars: # scriptingAfterBiases = off [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = "one"
colvars: Initializing a new "distance" component.
colvars: # name = "" [default]
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # forceNoPBC = off [default]
colvars: # scalable = on [default]
colvars: Initializing atom group "group1".
colvars: # name = "" [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
colvars: Initializing atom group "group2".
colvars: # name = "" [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 4, total charge = 0.
colvars: # oneSiteSystemForce = off [default]
colvars: # oneSiteTotalForce = off [default]
colvars: All components initialized.
colvars: # timeStepFactor = 1 [default]
colvars: # width = 1 [default]
colvars: # lowerBoundary = 0 [default]
colvars: # upperBoundary = 0 [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputTotalForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars: # subtractAppliedForce = off [default]
colvars: # runAve = off [default]
colvars: # corrFunc = off [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "harmonic" instance.
colvars: # name = "h_pot"
colvars: # colvars = { one }
colvars: # outputEnergy = off [default]
colvars: # timeStepFactor = 1 [default]
colvars: # writeTISamples = off [default]
colvars: # writeTIPMF = off [default]
colvars: # centers = { 10 }
colvars: # targetCenters = { 10 } [default]
colvars: # outputCenters = off [default]
colvars: # forceConstant = 100
colvars: # targetForceConstant = -1 [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables biases initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Collective variables module (re)initialized.
colvars: ----------------------------------------------------------------------
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 4.
colvars: The restart output state file will be "rest.colvars.state".
colvars: The final output state file will be "peptide2.colvars.state".
colvars: Writing to colvar trajectory file "peptide2.colvars.traj".
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 15.035.
colvars: Performing analysis.
SHAKE stats (type/ave/delta) on step 0
4 1.111 1.44264e-05
6 0.996998 7.26967e-06
8 1.08 1.32536e-05
10 1.111 1.22749e-05
12 1.08 1.11767e-05
14 0.96 0
18 0.957206 4.37979e-05
31 104.519 0.00396029
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
SHAKE stats (type/ave/delta) on step 100
4 1.11096 0.000191462
6 0.996989 3.55508e-05
8 1.08 9.0997e-06
10 1.111 1.58544e-05
12 1.08 5.80604e-06
14 0.959997 0
18 0.957198 2.92445e-05
31 104.52 0.00239923
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
colvars: Saving collective variables state to "peptide2.colvars.state".
Loop time of 2.25958 on 1 procs for 100 steps with 2004 atoms
Performance: 7.647 ns/day, 3.138 hours/ns, 44.256 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.6373 | 1.6373 | 1.6373 | 0.0 | 72.46
Bond | 0.0031531 | 0.0031531 | 0.0031531 | 0.0 | 0.14
Kspace | 0.17439 | 0.17439 | 0.17439 | 0.0 | 7.72
Neigh | 0.40442 | 0.40442 | 0.40442 | 0.0 | 17.90
Comm | 0.014091 | 0.014091 | 0.014091 | 0.0 | 0.62
Output | 0.00027752 | 0.00027752 | 0.00027752 | 0.0 | 0.01
Modify | 0.024481 | 0.024481 | 0.024481 | 0.0 | 1.08
Other | | 0.001465 | | | 0.06
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11143 ave 11143 max 11143 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 708234 ave 708234 max 708234 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708234
Ave neighs/atom = 353.41
Ave special neighs/atom = 2.34032
Neighbor list builds = 13
Dangerous builds = 1
colvars: Resetting the Collective Variables module.
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:02

260
examples/PACKAGES/colvars/log.27Nov18.peptide-colvars2.g++.4
View File

@ -1,260 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 2 by 2 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
group peptide type <= 12
84 atoms in group peptide
group one id 2 4 5 6
4 atoms in group one
group two id 80 82 83 84
4 atoms in group two
group ref id 37
1 atoms in group ref
group colvar union one two ref
9 atoms in group colvar
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
shell "rm -f peptide2.colvars.*"
fix 2 all colvars peptide.colvars2 output peptide2
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
thermo_style custom step temp etotal pe ke epair ebond f_2
thermo 10
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 4312 960
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
colvars: Creating proxy instance
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2018-11-16.
colvars: Please cite Fiorin et al, Mol Phys 2013:
colvars: https://doi.org/10.1080/00268976.2013.813594
colvars: in any publication based on this calculation.
colvars: SMP parallelism is available.
colvars: Using LAMMPS interface, version 2018-08-29.
colvars: ----------------------------------------------------------------------
colvars: Reading new configuration from file "peptide.colvars2":
colvars: # smp = on [default]
colvars: # colvarsTrajFrequency = 1
colvars: # colvarsRestartFrequency = 1000
colvars: # scriptedColvarForces = off [default]
colvars: # scriptingAfterBiases = off [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = "one"
colvars: Initializing a new "distance" component.
colvars: # name = "" [default]
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # forceNoPBC = off [default]
colvars: # scalable = on [default]
colvars: Initializing atom group "group1".
colvars: # name = "" [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
colvars: Initializing atom group "group2".
colvars: # name = "" [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # enableFitGradients = on [default]
colvars: # printAtomIDs = off [default]
colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 4, total charge = 0.
colvars: # oneSiteSystemForce = off [default]
colvars: # oneSiteTotalForce = off [default]
colvars: All components initialized.
colvars: # timeStepFactor = 1 [default]
colvars: # width = 1 [default]
colvars: # lowerBoundary = 0 [default]
colvars: # upperBoundary = 0 [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputTotalForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars: # subtractAppliedForce = off [default]
colvars: # runAve = off [default]
colvars: # corrFunc = off [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "harmonic" instance.
colvars: # name = "h_pot"
colvars: # colvars = { one }
colvars: # outputEnergy = off [default]
colvars: # timeStepFactor = 1 [default]
colvars: # writeTISamples = off [default]
colvars: # writeTIPMF = off [default]
colvars: # centers = { 10 }
colvars: # targetCenters = { 10 } [default]
colvars: # outputCenters = off [default]
colvars: # forceConstant = 100
colvars: # targetForceConstant = -1 [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables biases initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Collective variables module (re)initialized.
colvars: ----------------------------------------------------------------------
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 4.
colvars: The restart output state file will be "rest.colvars.state".
colvars: The final output state file will be "peptide2.colvars.state".
colvars: Writing to colvar trajectory file "peptide2.colvars.traj".
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 15.035.
colvars: Performing analysis.
SHAKE stats (type/ave/delta) on step 0
4 1.111 1.44264e-05
6 0.996998 7.26967e-06
8 1.08 1.32536e-05
10 1.111 1.22749e-05
12 1.08 1.11767e-05
14 0.96 0
18 0.957206 4.37979e-05
31 104.519 0.00396029
Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
SHAKE stats (type/ave/delta) on step 100
4 1.11096 0.000191462
6 0.996989 3.55508e-05
8 1.08 9.0997e-06
10 1.111 1.58544e-05
12 1.08 5.80604e-06
14 0.959997 0
18 0.957198 2.92445e-05
31 104.52 0.00239923
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
colvars: Saving collective variables state to "peptide2.colvars.state".
Loop time of 0.629325 on 4 procs for 100 steps with 2004 atoms
Performance: 27.458 ns/day, 0.874 hours/ns, 158.900 timesteps/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.4012 | 0.41532 | 0.42829 | 1.9 | 65.99
Bond | 0.0005219 | 0.0011545 | 0.0018291 | 1.8 | 0.18
Kspace | 0.059271 | 0.071301 | 0.084393 | 4.4 | 11.33
Neigh | 0.10416 | 0.10419 | 0.10424 | 0.0 | 16.56
Comm | 0.015643 | 0.016628 | 0.017256 | 0.5 | 2.64
Output | 0.00025177 | 0.00033599 | 0.00058722 | 0.0 | 0.05
Modify | 0.01912 | 0.019129 | 0.019141 | 0.0 | 3.04
Other | | 0.001264 | | | 0.20
Nlocal: 501 ave 513 max 494 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Nghost: 6572.5 ave 6593 max 6548 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 177058 ave 181778 max 174301 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 708234
Ave neighs/atom = 353.41
Ave special neighs/atom = 2.34032
Neighbor list builds = 13
Dangerous builds = 1
colvars: Resetting the Collective Variables module.
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

163
examples/PACKAGES/colvars/log.27Nov18.peptide-spring.g++.1
View File

@ -1,163 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 1 by 1 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
group peptide type <= 12
84 atoms in group peptide
group one id 2 4 5 6
4 atoms in group one
group two id 80 82 83 84
4 atoms in group two
group ref id 37
1 atoms in group ref
group colvar union one two ref
9 atoms in group colvar
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0
fix 2a ref setforce 0.0 0.0 0.0
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
#dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
variable sp equal f_3a+f_3b
thermo_style custom step temp etotal pe ke epair ebond v_sp
thermo 10
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 10648 3375
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
SHAKE stats (type/ave/delta) on step 0
4 1.111 1.44264e-05
6 0.996998 7.26967e-06
8 1.08 1.32536e-05
10 1.111 1.22749e-05
12 1.08 1.11767e-05
14 0.96 0
18 0.957206 4.37979e-05
31 104.519 0.00396029
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond v_sp
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
SHAKE stats (type/ave/delta) on step 100
4 1.11098 8.97155e-05
6 0.996996 1.00568e-05
8 1.08 6.02345e-06
10 1.111 1.84253e-05
12 1.08 7.2713e-06
14 0.959996 0
18 0.957198 3.36079e-05
31 104.52 0.0030599
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
Loop time of 2.21146 on 1 procs for 100 steps with 2004 atoms
Performance: 7.814 ns/day, 3.071 hours/ns, 45.219 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.6195 | 1.6195 | 1.6195 | 0.0 | 73.23
Bond | 0.0033534 | 0.0033534 | 0.0033534 | 0.0 | 0.15
Kspace | 0.17464 | 0.17464 | 0.17464 | 0.0 | 7.90
Neigh | 0.37337 | 0.37337 | 0.37337 | 0.0 | 16.88
Comm | 0.013891 | 0.013891 | 0.013891 | 0.0 | 0.63
Output | 0.00037336 | 0.00037336 | 0.00037336 | 0.0 | 0.02
Modify | 0.024753 | 0.024753 | 0.024753 | 0.0 | 1.12
Other | | 0.001613 | | | 0.07
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11124 ave 11124 max 11124 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 708237 ave 708237 max 708237 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708237
Ave neighs/atom = 353.412
Ave special neighs/atom = 2.34032
Neighbor list builds = 12
Dangerous builds = 2
Total wall time: 0:00:02

163
examples/PACKAGES/colvars/log.27Nov18.peptide-spring.g++.4
View File

@ -1,163 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 2 by 2 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
group peptide type <= 12
84 atoms in group peptide
group one id 2 4 5 6
4 atoms in group one
group two id 80 82 83 84
4 atoms in group two
group ref id 37
1 atoms in group ref
group colvar union one two ref
9 atoms in group colvar
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0
fix 2a ref setforce 0.0 0.0 0.0
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
#dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
variable sp equal f_3a+f_3b
thermo_style custom step temp etotal pe ke epair ebond v_sp
thermo 10
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 4312 960
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
SHAKE stats (type/ave/delta) on step 0
4 1.111 1.44264e-05
6 0.996998 7.26967e-06
8 1.08 1.32536e-05
10 1.111 1.22749e-05
12 1.08 1.11767e-05
14 0.96 0
18 0.957206 4.37979e-05
31 104.519 0.00396029
Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond v_sp
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
SHAKE stats (type/ave/delta) on step 100
4 1.11098 8.97155e-05
6 0.996996 1.00568e-05
8 1.08 6.02345e-06
10 1.111 1.84253e-05
12 1.08 7.2713e-06
14 0.959996 0
18 0.957198 3.36079e-05
31 104.52 0.0030599
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
Loop time of 0.620672 on 4 procs for 100 steps with 2004 atoms
Performance: 27.841 ns/day, 0.862 hours/ns, 161.116 timesteps/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.4029 | 0.41752 | 0.4307 | 1.7 | 67.27
Bond | 0.00054789 | 0.0011698 | 0.0018225 | 1.8 | 0.19
Kspace | 0.055853 | 0.069798 | 0.083975 | 4.3 | 11.25
Neigh | 0.096553 | 0.096622 | 0.096707 | 0.0 | 15.57
Comm | 0.015383 | 0.016022 | 0.01632 | 0.3 | 2.58
Output | 0.00033116 | 0.00057495 | 0.0012989 | 0.0 | 0.09
Modify | 0.017549 | 0.017693 | 0.017826 | 0.1 | 2.85
Other | | 0.001274 | | | 0.21
Nlocal: 501 ave 513 max 489 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 6563.25 ave 6596 max 6519 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 177059 ave 181742 max 172942 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 708237
Ave neighs/atom = 353.412
Ave special neighs/atom = 2.34032
Neighbor list builds = 12
Dangerous builds = 2
Total wall time: 0:00:00

158
examples/PACKAGES/colvars/log.27Nov18.peptide-spring2.g++.1
View File

@ -1,158 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 1 by 1 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
group peptide type <= 12
84 atoms in group peptide
group one id 2 4 5 6
4 atoms in group one
group two id 80 82 83 84
4 atoms in group two
group ref id 37
1 atoms in group ref
group colvar union one two ref
9 atoms in group colvar
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
#dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
thermo_style custom step temp etotal pe ke epair ebond f_3
thermo 10
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 10648 3375
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
SHAKE stats (type/ave/delta) on step 0
4 1.111 1.44264e-05
6 0.996998 7.26967e-06
8 1.08 1.32536e-05
10 1.111 1.22749e-05
12 1.08 1.11767e-05
14 0.96 0
18 0.957206 4.37979e-05
31 104.519 0.00396029
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_3
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
SHAKE stats (type/ave/delta) on step 100
4 1.11096 0.000191462
6 0.996989 3.55508e-05
8 1.08 9.0997e-06
10 1.111 1.58544e-05
12 1.08 5.80604e-06
14 0.959997 0
18 0.957198 2.92445e-05
31 104.52 0.00239923
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
Loop time of 2.2037 on 1 procs for 100 steps with 2004 atoms
Performance: 7.841 ns/day, 3.061 hours/ns, 45.378 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.5852 | 1.5852 | 1.5852 | 0.0 | 71.93
Bond | 0.0032725 | 0.0032725 | 0.0032725 | 0.0 | 0.15
Kspace | 0.17308 | 0.17308 | 0.17308 | 0.0 | 7.85
Neigh | 0.4027 | 0.4027 | 0.4027 | 0.0 | 18.27
Comm | 0.014041 | 0.014041 | 0.014041 | 0.0 | 0.64
Output | 0.00032306 | 0.00032306 | 0.00032306 | 0.0 | 0.01
Modify | 0.023546 | 0.023546 | 0.023546 | 0.0 | 1.07
Other | | 0.001546 | | | 0.07
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11143 ave 11143 max 11143 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 708234 ave 708234 max 708234 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708234
Ave neighs/atom = 353.41
Ave special neighs/atom = 2.34032
Neighbor list builds = 13
Dangerous builds = 1
Total wall time: 0:00:02

158
examples/PACKAGES/colvars/log.27Nov18.peptide-spring2.g++.4
View File

@ -1,158 +0,0 @@
LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 2 by 2 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
group peptide type <= 12
84 atoms in group peptide
group one id 2 4 5 6
4 atoms in group one
group two id 80 82 83 84
4 atoms in group two
group ref id 37
1 atoms in group ref
group colvar union one two ref
9 atoms in group colvar
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
#dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
thermo_style custom step temp etotal pe ke epair ebond f_3
thermo 10
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 4312 960
Neighbor list info ...
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
SHAKE stats (type/ave/delta) on step 0
4 1.111 1.44264e-05
6 0.996998 7.26967e-06
8 1.08 1.32536e-05
10 1.111 1.22749e-05
12 1.08 1.11767e-05
14 0.96 0
18 0.957206 4.37979e-05
31 104.519 0.00396029
Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_3
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
SHAKE stats (type/ave/delta) on step 100
4 1.11096 0.000191462
6 0.996989 3.55508e-05
8 1.08 9.0997e-06
10 1.111 1.58544e-05
12 1.08 5.80604e-06
14 0.959997 0
18 0.957198 2.92445e-05
31 104.52 0.00239923
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
Loop time of 0.616036 on 4 procs for 100 steps with 2004 atoms
Performance: 28.050 ns/day, 0.856 hours/ns, 162.328 timesteps/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.40372 | 0.41244 | 0.41714 | 0.8 | 66.95
Bond | 0.00053573 | 0.0011384 | 0.0017946 | 1.8 | 0.18
Kspace | 0.060087 | 0.063993 | 0.07306 | 2.1 | 10.39
Neigh | 0.1033 | 0.10349 | 0.1036 | 0.0 | 16.80
Comm | 0.01568 | 0.016453 | 0.017178 | 0.5 | 2.67
Output | 0.00028253 | 0.00032026 | 0.00043178 | 0.0 | 0.05
Modify | 0.016238 | 0.016955 | 0.017704 | 0.5 | 2.75
Other | | 0.001239 | | | 0.20
Nlocal: 501 ave 513 max 494 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Nghost: 6572.5 ave 6593 max 6548 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 177058 ave 181778 max 174301 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 708234
Ave neighs/atom = 353.41
Ave special neighs/atom = 2.34032
Neighbor list builds = 13
Dangerous builds = 1
Total wall time: 0:00:00

732
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars.g++.1 Normal file
View File

@ -0,0 +1,732 @@
LAMMPS (27 Jun 2024)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
Reading data file ...
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
1 by 1 by 1 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
1 by 1 by 1 MPI processor grid
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.012 seconds
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
group peptide type <= 12
84 atoms in group peptide
group one id 2 4 5 6
4 atoms in group one
group two id 80 82 83 84
4 atoms in group two
group ref id 37
1 atoms in group ref
group colvar union one two ref
9 atoms in group colvar
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
shell "rm -f out*.colvars.*"
fix 2 all colvars peptide.colvars
----------------------------------------------------------------------
Initializing the collective variables module, version 2024-06-04.
Please cite Fiorin et al, Mol Phys 2013:
https://doi.org/10.1080/00268976.2013.813594
as well as all other papers listed below for individual features used.
Please cite Fiorin et al, Mol Phys 2013:
https://doi.org/10.1080/00268976.2013.813594
as well as all other papers listed below for individual features used.
Please cite Fiorin et al, Mol Phys 2013:
https://doi.org/10.1080/00268976.2013.813594
as well as all other papers listed below for individual features used.
This version was built with the C++11 standard or higher.
Summary of compile-time features available in this build:
- SMP parallelism: enabled (num. threads = 1)
- Lepton custom functions: available
- Tcl interpreter: not available
Using LAMMPS interface, version "2024-07-05".
fix 2a ref setforce 0.0 0.0 0.0
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
Finding SHAKE clusters ...
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
find clusters CPU = 0.000 seconds
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
thermo_style custom step temp etotal pe ke epair ebond f_2
thermo 10
run 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
@Article{Gissinger24,
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
journal = {J. Phys. Chem. B},
year = 2024,
volume = 128,
number = 13,
pages = {3282–-3297}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.26872465
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.022820853
estimated relative force accuracy = 6.872432e-05
using double precision FFTW3
3d grid and FFT values/proc = 10648 3375
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 5 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
----------------------------------------------------------------------
Reading new configuration from file "peptide.colvars":
# units = "" [default]
# smp = on [default]
# colvarsTrajFrequency = 1
# colvarsRestartFrequency = 1000
# scriptedColvarForces = off [default]
# scriptingAfterBiases = off [default]
----------------------------------------------------------------------
Initializing a new collective variable.
# name = "one"
Initializing a new "distance" component.
# name = "" [default]
# componentCoeff = 1 [default]
# componentExp = 1 [default]
# period = 0 [default]
# wrapAround = 0 [default]
# forceNoPBC = off [default]
# scalable = on [default]
Initializing atom group "group1".
# name = "" [default]
# centerToOrigin = off [default]
# centerToReference = off [default]
# rotateToReference = off [default]
# atomsOfGroup = "" [default]
# indexGroup = "" [default]
# psfSegID = [default]
# atomsFile = "" [default]
# dummyAtom = ( 0 , 0 , 0 ) [default]
# enableFitGradients = on [default]
# printAtomIDs = off [default]
Atom group "group1" defined with 4 atoms requested.
Initializing atom group "group2".
# name = "" [default]
# centerToOrigin = off [default]
# centerToReference = off [default]
# rotateToReference = off [default]
# atomsOfGroup = "" [default]
# indexGroup = "" [default]
# psfSegID = [default]
# atomsFile = "" [default]
# dummyAtom = ( 0 , 0 , 0 ) [default]
# enableFitGradients = on [default]
# printAtomIDs = off [default]
Atom group "group2" defined with 1 atoms requested.
# oneSiteSystemForce = off [default]
# oneSiteTotalForce = off [default]
All components initialized.
# timeStepFactor = 1 [default]
# width = 1 [default]
# lowerBoundary = 0 [default]
# upperBoundary = 1 [default]
# hardLowerBoundary = on [default]
# hardUpperBoundary = off [default]
# expandBoundaries = off [default]
# extendedLagrangian = off [default]
# outputValue = on [default]
# outputVelocity = off [default]
# outputTotalForce = off [default]
# outputAppliedForce = off [default]
# subtractAppliedForce = off [default]
# runAve = off [default]
# corrFunc = off [default]
----------------------------------------------------------------------
Initializing a new collective variable.
# name = "two"
Initializing a new "distance" component.
# name = "" [default]
# componentCoeff = 1 [default]
# componentExp = 1 [default]
# period = 0 [default]
# wrapAround = 0 [default]
# forceNoPBC = off [default]
# scalable = on [default]
Initializing atom group "group1".
# name = "" [default]
# centerToOrigin = off [default]
# centerToReference = off [default]
# rotateToReference = off [default]
# atomsOfGroup = "" [default]
# indexGroup = "" [default]
# psfSegID = [default]
# atomsFile = "" [default]
# dummyAtom = ( 0 , 0 , 0 ) [default]
# enableFitGradients = on [default]
# printAtomIDs = off [default]
Atom group "group1" defined with 4 atoms requested.
Initializing atom group "group2".
# name = "" [default]
# centerToOrigin = off [default]
# centerToReference = off [default]
# rotateToReference = off [default]
# atomsOfGroup = "" [default]
# indexGroup = "" [default]
# psfSegID = [default]
# atomsFile = "" [default]
# dummyAtom = ( 0 , 0 , 0 ) [default]
# enableFitGradients = on [default]
# printAtomIDs = off [default]
Atom group "group2" defined with 1 atoms requested.
# oneSiteSystemForce = off [default]
# oneSiteTotalForce = off [default]
All components initialized.
# timeStepFactor = 1 [default]
# width = 1 [default]
# lowerBoundary = 0 [default]
# upperBoundary = 1 [default]
# hardLowerBoundary = on [default]
# hardUpperBoundary = off [default]
# expandBoundaries = off [default]
# extendedLagrangian = off [default]
# outputValue = on [default]
# outputVelocity = off [default]
# outputTotalForce = off [default]
# outputAppliedForce = off [default]
# subtractAppliedForce = off [default]
# runAve = off [default]
# corrFunc = off [default]
----------------------------------------------------------------------
Collective variables initialized, 2 in total.
----------------------------------------------------------------------
Initializing a new "harmonic" instance.
# name = "h_pot"
# colvars = { one, two }
# stepZeroData = off [default]
# outputEnergy = off [default]
# outputFreq = 1000 [default]
# timeStepFactor = 1 [default]
# writeTISamples = off [default]
# writeTIPMF = off [default]
# centers = { 10, 10 }
# targetCenters = { 10, 10 } [default]
# outputCenters = off [default]
# forceConstant = 100
# decoupling = off [default]
# targetForceConstant = -1 [default]
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
The force constant for colvar "two" will be rescaled to 100 according to the specified width (1).
----------------------------------------------------------------------
Collective variables biases initialized, 1 in total.
----------------------------------------------------------------------
Collective variables module (re)initialized.
----------------------------------------------------------------------
Current simulation parameters: initial step = 0, integration timestep = 2
Updating atomic parameters (masses, charges, etc).
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
The final output state file will be "out.colvars.state".
Synchronizing (emptying the buffer of) trajectory file "out.colvars.traj".
SHAKE stats (type/ave/delta/count) on step 0
Bond: 4 1.111 1.44264e-05 9
Bond: 6 0.996998 7.26967e-06 6
Bond: 8 1.08 1.32536e-05 7
Bond: 10 1.111 1.22749e-05 8
Bond: 12 1.08 1.11767e-05 9
Bond: 14 0.96 0 1
Bond: 18 0.957206 4.37979e-05 1280
Angle: 31 104.519 0.00396029 640
Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
SHAKE stats (type/ave/delta/count) on step 100
Bond: 4 1.11098 8.97155e-05 9
Bond: 6 0.996996 1.00568e-05 6
Bond: 8 1.08 6.02345e-06 7
Bond: 10 1.111 1.84253e-05 8
Bond: 12 1.08 7.2713e-06 9
Bond: 14 0.959996 0 1
Bond: 18 0.957198 3.36079e-05 1280
Angle: 31 104.52 0.0030599 640
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
Saving collective variables state to "out.colvars.state".
Loop time of 0.897199 on 1 procs for 100 steps with 2004 atoms
Performance: 19.260 ns/day, 1.246 hours/ns, 111.458 timesteps/s, 223.362 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.71298 | 0.71298 | 0.71298 | 0.0 | 79.47
Bond | 0.001284 | 0.001284 | 0.001284 | 0.0 | 0.14
Kspace | 0.041232 | 0.041232 | 0.041232 | 0.0 | 4.60
Neigh | 0.1277 | 0.1277 | 0.1277 | 0.0 | 14.23
Comm | 0.0033285 | 0.0033285 | 0.0033285 | 0.0 | 0.37
Output | 0.00017467 | 0.00017467 | 0.00017467 | 0.0 | 0.02
Modify | 0.010003 | 0.010003 | 0.010003 | 0.0 | 1.11
Other | | 0.0004941 | | | 0.06
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11124 ave 11124 max 11124 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 708237 ave 708237 max 708237 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708237
Ave neighs/atom = 353.41168
Ave special neighs/atom = 2.3403194
Neighbor list builds = 12
Dangerous builds = 2
run 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Colvars module (Fiorin2013, plus other works listed for specific features)
% Colvars module:
% Colvars-LAMMPS interface:
% Harmonic colvar bias implementation:
% Optimal rotation via flexible fitting:
% distance colvar component:
@article{Fiorin2013,
author = {Fiorin, Giacomo and Klein, Michael L.{} and H\'enin, J\'er\^ome},
title = {Using collective variables to drive molecular dynamics simulations},
journal = {Mol. Phys.},
year = {2013},
volume = {111},
number = {22-23},
pages = {3345--3362},
publisher = {Taylor & Francis},
doi = {10.1080/00268976.2013.813594},
url = {https://doi.org/10.1080/00268976.2013.813594}
}
% LAMMPS engine:
@article{Thompson2022,
title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and {in't Veld}, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.},
journal = {Comp. Phys. Comm.},
volume = {271},
pages = {108171},
year = {2022},
doi = {10.1016/j.cpc.2021.108171},
url = {https://doi.org/10.1016/j.cpc.2021.108171}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.26872465
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.022820853
estimated relative force accuracy = 6.872432e-05
using double precision FFTW3
3d grid and FFT values/proc = 10648 3375
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
Current simulation parameters: initial step = 100, integration timestep = 2
Updating atomic parameters (masses, charges, etc).
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
SHAKE stats (type/ave/delta/count) on step 100
Bond: 4 1.11098 8.97155e-05 9
Bond: 6 0.996996 1.00568e-05 6
Bond: 8 1.08 6.02345e-06 7
Bond: 10 1.111 1.84253e-05 8
Bond: 12 1.08 7.2713e-06 9
Bond: 14 0.959996 0 1
Bond: 18 0.957198 3.36079e-05 1280
Angle: 31 104.52 0.0030599 640
Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657
120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812
130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031591
140 253.85111 -5452.1838 -6473.4521 1021.2684 -6609.4826 26.071651 0.30585517
150 261.31816 -5490.4726 -6541.7817 1051.3091 -6646.6075 16.258823 6.9051008
160 255.7352 -5521.5941 -6550.4423 1028.8483 -6658.1372 19.717399 12.339679
170 253.42527 -5540.0942 -6559.6494 1019.5552 -6656.6678 23.293812 10.290217
180 248.51161 -5550.3254 -6550.1125 999.78704 -6661.4236 26.200127 3.4336037
190 250.80862 -5555.2554 -6564.2836 1009.0281 -6666.164 25.53634 3.3494286
SHAKE stats (type/ave/delta/count) on step 200
Bond: 4 1.111 1.81266e-06 9
Bond: 6 0.997 7.79424e-07 6
Bond: 8 1.08 1.08903e-06 7
Bond: 10 1.111 2.96503e-07 8
Bond: 12 1.08 4.69038e-07 9
Bond: 14 0.960001 0 1
Bond: 18 0.957201 3.76471e-06 1280
Angle: 31 104.52 0.000411055 640
200 251.50475 -5557.4251 -6569.2538 1011.8288 -6674.0845 24.804906 7.1387572
Saving collective variables state to "out.colvars.state".
Loop time of 0.855092 on 1 procs for 100 steps with 2004 atoms
Performance: 20.208 ns/day, 1.188 hours/ns, 116.946 timesteps/s, 234.361 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.71954 | 0.71954 | 0.71954 | 0.0 | 84.15
Bond | 0.0012655 | 0.0012655 | 0.0012655 | 0.0 | 0.15
Kspace | 0.042826 | 0.042826 | 0.042826 | 0.0 | 5.01
Neigh | 0.078128 | 0.078128 | 0.078128 | 0.0 | 9.14
Comm | 0.0029003 | 0.0029003 | 0.0029003 | 0.0 | 0.34
Output | 0.00016605 | 0.00016605 | 0.00016605 | 0.0 | 0.02
Modify | 0.0097753 | 0.0097753 | 0.0097753 | 0.0 | 1.14
Other | | 0.0004882 | | | 0.06
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11159 ave 11159 max 11159 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 708083 ave 708083 max 708083 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708083
Ave neighs/atom = 353.33483
Ave special neighs/atom = 2.3403194
Neighbor list builds = 7
Dangerous builds = 0
fix 2 all colvars peptide.colvars input out.colvars.state output out2
----------------------------------------------------------------------
Initializing the collective variables module, version 2024-06-04.
Please cite Fiorin et al, Mol Phys 2013:
https://doi.org/10.1080/00268976.2013.813594
as well as all other papers listed below for individual features used.
Please cite Fiorin et al, Mol Phys 2013:
https://doi.org/10.1080/00268976.2013.813594
as well as all other papers listed below for individual features used.
Please cite Fiorin et al, Mol Phys 2013:
https://doi.org/10.1080/00268976.2013.813594
as well as all other papers listed below for individual features used.
This version was built with the C++11 standard or higher.
Summary of compile-time features available in this build:
- SMP parallelism: enabled (num. threads = 1)
- Lepton custom functions: available
- Tcl interpreter: not available
Using LAMMPS interface, version "2024-07-05".
Setting initial step number from MD engine: 200
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.26872465
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.022820853
estimated relative force accuracy = 6.872432e-05
using double precision FFTW3
3d grid and FFT values/proc = 10648 3375
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
Will read input state from file "out.colvars.state"----------------------------------------------------------------------
Reading new configuration from file "peptide.colvars":
# units = "" [default]
# smp = on [default]
# colvarsTrajFrequency = 1
# colvarsRestartFrequency = 1000
# scriptedColvarForces = off [default]
# scriptingAfterBiases = off [default]
----------------------------------------------------------------------
Initializing a new collective variable.
# name = "one"
Initializing a new "distance" component.
# name = "" [default]
# componentCoeff = 1 [default]
# componentExp = 1 [default]
# period = 0 [default]
# wrapAround = 0 [default]
# forceNoPBC = off [default]
# scalable = on [default]
Initializing atom group "group1".
# name = "" [default]
# centerToOrigin = off [default]
# centerToReference = off [default]
# rotateToReference = off [default]
# atomsOfGroup = "" [default]
# indexGroup = "" [default]
# psfSegID = [default]
# atomsFile = "" [default]
# dummyAtom = ( 0 , 0 , 0 ) [default]
# enableFitGradients = on [default]
# printAtomIDs = off [default]
Atom group "group1" defined with 4 atoms requested.
Initializing atom group "group2".
# name = "" [default]
# centerToOrigin = off [default]
# centerToReference = off [default]
# rotateToReference = off [default]
# atomsOfGroup = "" [default]
# indexGroup = "" [default]
# psfSegID = [default]
# atomsFile = "" [default]
# dummyAtom = ( 0 , 0 , 0 ) [default]
# enableFitGradients = on [default]
# printAtomIDs = off [default]
Atom group "group2" defined with 1 atoms requested.
# oneSiteSystemForce = off [default]
# oneSiteTotalForce = off [default]
All components initialized.
# timeStepFactor = 1 [default]
# width = 1 [default]
# lowerBoundary = 0 [default]
# upperBoundary = 1 [default]
# hardLowerBoundary = on [default]
# hardUpperBoundary = off [default]
# expandBoundaries = off [default]
# extendedLagrangian = off [default]
# outputValue = on [default]
# outputVelocity = off [default]
# outputTotalForce = off [default]
# outputAppliedForce = off [default]
# subtractAppliedForce = off [default]
# runAve = off [default]
# corrFunc = off [default]
----------------------------------------------------------------------
Initializing a new collective variable.
# name = "two"
Initializing a new "distance" component.
# name = "" [default]
# componentCoeff = 1 [default]
# componentExp = 1 [default]
# period = 0 [default]
# wrapAround = 0 [default]
# forceNoPBC = off [default]
# scalable = on [default]
Initializing atom group "group1".
# name = "" [default]
# centerToOrigin = off [default]
# centerToReference = off [default]
# rotateToReference = off [default]
# atomsOfGroup = "" [default]
# indexGroup = "" [default]
# psfSegID = [default]
# atomsFile = "" [default]
# dummyAtom = ( 0 , 0 , 0 ) [default]
# enableFitGradients = on [default]
# printAtomIDs = off [default]
Atom group "group1" defined with 4 atoms requested.
Initializing atom group "group2".
# name = "" [default]
# centerToOrigin = off [default]
# centerToReference = off [default]
# rotateToReference = off [default]
# atomsOfGroup = "" [default]
# indexGroup = "" [default]
# psfSegID = [default]
# atomsFile = "" [default]
# dummyAtom = ( 0 , 0 , 0 ) [default]
# enableFitGradients = on [default]
# printAtomIDs = off [default]
Atom group "group2" defined with 1 atoms requested.
# oneSiteSystemForce = off [default]
# oneSiteTotalForce = off [default]
All components initialized.
# timeStepFactor = 1 [default]
# width = 1 [default]
# lowerBoundary = 0 [default]
# upperBoundary = 1 [default]
# hardLowerBoundary = on [default]
# hardUpperBoundary = off [default]
# expandBoundaries = off [default]
# extendedLagrangian = off [default]
# outputValue = on [default]
# outputVelocity = off [default]
# outputTotalForce = off [default]
# outputAppliedForce = off [default]
# subtractAppliedForce = off [default]
# runAve = off [default]
# corrFunc = off [default]
----------------------------------------------------------------------
Collective variables initialized, 2 in total.
----------------------------------------------------------------------
Initializing a new "harmonic" instance.
# name = "h_pot"
# colvars = { one, two }
# stepZeroData = off [default]
# outputEnergy = off [default]
# outputFreq = 1000 [default]
# timeStepFactor = 1 [default]
# writeTISamples = off [default]
# writeTIPMF = off [default]
# centers = { 10, 10 }
# targetCenters = { 10, 10 } [default]
# outputCenters = off [default]
# forceConstant = 100
# decoupling = off [default]
# targetForceConstant = -1 [default]
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
The force constant for colvar "two" will be rescaled to 100 according to the specified width (1).
----------------------------------------------------------------------
Collective variables biases initialized, 1 in total.
----------------------------------------------------------------------
Collective variables module (re)initialized.
----------------------------------------------------------------------
Current simulation parameters: initial step = 200, integration timestep = 2
Updating atomic parameters (masses, charges, etc).
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
----------------------------------------------------------------------
Loading state from text file "out.colvars.state".
Restarting collective variable "one" from value: 10.0128
Restarting collective variable "two" from value: 9.62236
Restarted harmonic bias "h_pot" with step number 200.
----------------------------------------------------------------------
The final output state file will be "out2.colvars.state".
SHAKE stats (type/ave/delta/count) on step 200
Bond: 4 1.111 1.81266e-06 9
Bond: 6 0.997 7.79424e-07 6
Bond: 8 1.08 1.08903e-06 7
Bond: 10 1.111 2.96503e-07 8
Bond: 12 1.08 4.69038e-07 9
Bond: 14 0.960001 0 1
Bond: 18 0.957201 3.76471e-06 1280
Angle: 31 104.52 0.000411055 640
Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
200 251.50475 -5557.4251 -6569.2538 1011.8288 -6674.0845 24.804906 7.1387572
210 253.15302 -5538.5614 -6557.0213 1018.4599 -6672.0496 37.676621 0.61219488
220 245.19621 -5522.5192 -6508.9681 986.44887 -6628.19 36.657688 0.048643387
230 258.69885 -5495.7277 -6536.499 1040.7713 -6658.2888 34.857911 0.2209256
240 260.79633 -5469.8678 -6519.0775 1049.2097 -6624.1799 31.576952 3.7574815
250 269.07527 -5438.3947 -6520.9114 1082.5167 -6616.4383 25.447674 8.6600023
260 266.01046 -5397.3484 -6467.5351 1070.1867 -6580.2895 26.871919 8.3323102
270 272.81307 -5350.882 -6448.4362 1097.5543 -6563.8228 23.114196 10.973132
280 279.42264 -5307.9798 -6432.125 1124.1452 -6557.3367 33.644021 8.5490492
290 286.85168 -5260.8411 -6414.874 1154.033 -6515.6797 28.574838 5.9100104
SHAKE stats (type/ave/delta/count) on step 300
Bond: 4 1.111 1.79793e-05 9
Bond: 6 0.997005 1.02512e-05 6
Bond: 8 1.08 1.85103e-05 7
Bond: 10 1.111 9.9884e-06 8
Bond: 12 1.08 8.84114e-06 9
Bond: 14 0.960008 0 1
Bond: 18 0.957203 1.8445e-05 1280
Angle: 31 104.52 0.00168383 640
300 291.52794 -5216.288 -6389.1341 1172.846 -6503.1276 27.889149 2.2482427
Saving collective variables state to "out2.colvars.state".
Loop time of 0.86889 on 1 procs for 100 steps with 2004 atoms
Performance: 19.887 ns/day, 1.207 hours/ns, 115.089 timesteps/s, 230.639 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.72728 | 0.72728 | 0.72728 | 0.0 | 83.70
Bond | 0.0012755 | 0.0012755 | 0.0012755 | 0.0 | 0.15
Kspace | 0.041631 | 0.041631 | 0.041631 | 0.0 | 4.79
Neigh | 0.085283 | 0.085283 | 0.085283 | 0.0 | 9.82
Comm | 0.0029986 | 0.0029986 | 0.0029986 | 0.0 | 0.35
Output | 0.00013272 | 0.00013272 | 0.00013272 | 0.0 | 0.02
Modify | 0.0097972 | 0.0097972 | 0.0097972 | 0.0 | 1.13
Other | | 0.0004882 | | | 0.06
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11296 ave 11296 max 11296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 708152 ave 708152 max 708152 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708152
Ave neighs/atom = 353.36926
Ave special neighs/atom = 2.3403194
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:02

732
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars.g++.4 Normal file
View File

@ -0,0 +1,732 @@
LAMMPS (27 Jun 2024)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
Reading data file ...
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
1 by 2 by 2 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
1 by 2 by 2 MPI processor grid
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.011 seconds
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
group peptide type <= 12
84 atoms in group peptide
group one id 2 4 5 6
4 atoms in group one
group two id 80 82 83 84
4 atoms in group two
group ref id 37
1 atoms in group ref
group colvar union one two ref
9 atoms in group colvar
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
shell "rm -f out*.colvars.*"
fix 2 all colvars peptide.colvars
----------------------------------------------------------------------
Initializing the collective variables module, version 2024-06-04.
Please cite Fiorin et al, Mol Phys 2013:
https://doi.org/10.1080/00268976.2013.813594
as well as all other papers listed below for individual features used.
Please cite Fiorin et al, Mol Phys 2013:
https://doi.org/10.1080/00268976.2013.813594
as well as all other papers listed below for individual features used.
Please cite Fiorin et al, Mol Phys 2013:
https://doi.org/10.1080/00268976.2013.813594
as well as all other papers listed below for individual features used.
This version was built with the C++11 standard or higher.
Summary of compile-time features available in this build:
- SMP parallelism: enabled (num. threads = 1)
- Lepton custom functions: available
- Tcl interpreter: not available
Using LAMMPS interface, version "2024-07-05".
fix 2a ref setforce 0.0 0.0 0.0
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
Finding SHAKE clusters ...
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
find clusters CPU = 0.000 seconds
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
thermo_style custom step temp etotal pe ke epair ebond f_2
thermo 10
run 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
@Article{Gissinger24,
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
journal = {J. Phys. Chem. B},
year = 2024,
volume = 128,
number = 13,
pages = {3282–-3297}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.26872465
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.022820853
estimated relative force accuracy = 6.872432e-05
using double precision FFTW3
3d grid and FFT values/proc = 4312 960
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 5 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
----------------------------------------------------------------------
Reading new configuration from file "peptide.colvars":
# units = "" [default]
# smp = on [default]
# colvarsTrajFrequency = 1
# colvarsRestartFrequency = 1000
# scriptedColvarForces = off [default]
# scriptingAfterBiases = off [default]
----------------------------------------------------------------------
Initializing a new collective variable.
# name = "one"
Initializing a new "distance" component.
# name = "" [default]
# componentCoeff = 1 [default]
# componentExp = 1 [default]
# period = 0 [default]
# wrapAround = 0 [default]
# forceNoPBC = off [default]
# scalable = on [default]
Initializing atom group "group1".
# name = "" [default]
# centerToOrigin = off [default]
# centerToReference = off [default]
# rotateToReference = off [default]
# atomsOfGroup = "" [default]
# indexGroup = "" [default]
# psfSegID = [default]
# atomsFile = "" [default]
# dummyAtom = ( 0 , 0 , 0 ) [default]
# enableFitGradients = on [default]
# printAtomIDs = off [default]
Atom group "group1" defined with 4 atoms requested.
Initializing atom group "group2".
# name = "" [default]
# centerToOrigin = off [default]
# centerToReference = off [default]
# rotateToReference = off [default]
# atomsOfGroup = "" [default]
# indexGroup = "" [default]
# psfSegID = [default]
# atomsFile = "" [default]
# dummyAtom = ( 0 , 0 , 0 ) [default]
# enableFitGradients = on [default]
# printAtomIDs = off [default]
Atom group "group2" defined with 1 atoms requested.
# oneSiteSystemForce = off [default]
# oneSiteTotalForce = off [default]
All components initialized.
# timeStepFactor = 1 [default]
# width = 1 [default]
# lowerBoundary = 0 [default]
# upperBoundary = 1 [default]
# hardLowerBoundary = on [default]
# hardUpperBoundary = off [default]
# expandBoundaries = off [default]
# extendedLagrangian = off [default]
# outputValue = on [default]
# outputVelocity = off [default]
# outputTotalForce = off [default]
# outputAppliedForce = off [default]
# subtractAppliedForce = off [default]
# runAve = off [default]
# corrFunc = off [default]
----------------------------------------------------------------------
Initializing a new collective variable.
# name = "two"
Initializing a new "distance" component.
# name = "" [default]
# componentCoeff = 1 [default]
# componentExp = 1 [default]
# period = 0 [default]
# wrapAround = 0 [default]
# forceNoPBC = off [default]
# scalable = on [default]
Initializing atom group "group1".
# name = "" [default]
# centerToOrigin = off [default]
# centerToReference = off [default]
# rotateToReference = off [default]
# atomsOfGroup = "" [default]
# indexGroup = "" [default]
# psfSegID = [default]
# atomsFile = "" [default]
# dummyAtom = ( 0 , 0 , 0 ) [default]
# enableFitGradients = on [default]
# printAtomIDs = off [default]
Atom group "group1" defined with 4 atoms requested.
Initializing atom group "group2".
# name = "" [default]
# centerToOrigin = off [default]
# centerToReference = off [default]
# rotateToReference = off [default]
# atomsOfGroup = "" [default]
# indexGroup = "" [default]
# psfSegID = [default]
# atomsFile = "" [default]
# dummyAtom = ( 0 , 0 , 0 ) [default]
# enableFitGradients = on [default]
# printAtomIDs = off [default]
Atom group "group2" defined with 1 atoms requested.
# oneSiteSystemForce = off [default]
# oneSiteTotalForce = off [default]
All components initialized.
# timeStepFactor = 1 [default]
# width = 1 [default]
# lowerBoundary = 0 [default]
# upperBoundary = 1 [default]
# hardLowerBoundary = on [default]
# hardUpperBoundary = off [default]
# expandBoundaries = off [default]
# extendedLagrangian = off [default]
# outputValue = on [default]
# outputVelocity = off [default]
# outputTotalForce = off [default]
# outputAppliedForce = off [default]
# subtractAppliedForce = off [default]
# runAve = off [default]
# corrFunc = off [default]
----------------------------------------------------------------------
Collective variables initialized, 2 in total.
----------------------------------------------------------------------
Initializing a new "harmonic" instance.
# name = "h_pot"
# colvars = { one, two }
# stepZeroData = off [default]
# outputEnergy = off [default]
# outputFreq = 1000 [default]
# timeStepFactor = 1 [default]
# writeTISamples = off [default]
# writeTIPMF = off [default]
# centers = { 10, 10 }
# targetCenters = { 10, 10 } [default]
# outputCenters = off [default]
# forceConstant = 100
# decoupling = off [default]
# targetForceConstant = -1 [default]
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
The force constant for colvar "two" will be rescaled to 100 according to the specified width (1).
----------------------------------------------------------------------
Collective variables biases initialized, 1 in total.
----------------------------------------------------------------------
Collective variables module (re)initialized.
----------------------------------------------------------------------
Current simulation parameters: initial step = 0, integration timestep = 2
Updating atomic parameters (masses, charges, etc).
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
The final output state file will be "out.colvars.state".
Synchronizing (emptying the buffer of) trajectory file "out.colvars.traj".
SHAKE stats (type/ave/delta/count) on step 0
Bond: 4 1.111 1.44264e-05 9
Bond: 6 0.996998 7.26967e-06 6
Bond: 8 1.08 1.32536e-05 7
Bond: 10 1.111 1.22749e-05 8
Bond: 12 1.08 1.11767e-05 9
Bond: 14 0.96 0 1
Bond: 18 0.957206 4.37979e-05 1280
Angle: 31 104.519 0.00396029 640
Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.22 | 16.41 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
SHAKE stats (type/ave/delta/count) on step 100
Bond: 4 1.11098 8.97155e-05 9
Bond: 6 0.996996 1.00568e-05 6
Bond: 8 1.08 6.02345e-06 7
Bond: 10 1.111 1.84253e-05 8
Bond: 12 1.08 7.2713e-06 9
Bond: 14 0.959996 0 1
Bond: 18 0.957198 3.36079e-05 1280
Angle: 31 104.52 0.0030599 640
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
Saving collective variables state to "out.colvars.state".
Loop time of 0.246405 on 4 procs for 100 steps with 2004 atoms
Performance: 70.128 ns/day, 0.342 hours/ns, 405.836 timesteps/s, 813.295 katom-step/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.17765 | 0.18092 | 0.18373 | 0.6 | 73.42
Bond | 0.00021581 | 0.00045219 | 0.00069916 | 0.0 | 0.18
Kspace | 0.018035 | 0.020459 | 0.023812 | 1.7 | 8.30
Neigh | 0.032165 | 0.032193 | 0.032207 | 0.0 | 13.07
Comm | 0.00566 | 0.0058533 | 0.0060088 | 0.2 | 2.38
Output | 0.00012205 | 0.00014069 | 0.00019404 | 0.0 | 0.06
Modify | 0.0059979 | 0.0060225 | 0.0060368 | 0.0 | 2.44
Other | | 0.0003631 | | | 0.15
Nlocal: 501 ave 513 max 489 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 6563.25 ave 6596 max 6519 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 177059 ave 181742 max 172942 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 708237
Ave neighs/atom = 353.41168
Ave special neighs/atom = 2.3403194
Neighbor list builds = 12
Dangerous builds = 2
run 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Colvars module (Fiorin2013, plus other works listed for specific features)
% Colvars module:
% Colvars-LAMMPS interface:
% Harmonic colvar bias implementation:
% Optimal rotation via flexible fitting:
% distance colvar component:
@article{Fiorin2013,
author = {Fiorin, Giacomo and Klein, Michael L.{} and H\'enin, J\'er\^ome},
title = {Using collective variables to drive molecular dynamics simulations},
journal = {Mol. Phys.},
year = {2013},
volume = {111},
number = {22-23},
pages = {3345--3362},
publisher = {Taylor & Francis},
doi = {10.1080/00268976.2013.813594},
url = {https://doi.org/10.1080/00268976.2013.813594}
}
% LAMMPS engine:
@article{Thompson2022,
title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and {in't Veld}, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.},
journal = {Comp. Phys. Comm.},
volume = {271},
pages = {108171},
year = {2022},
doi = {10.1016/j.cpc.2021.108171},
url = {https://doi.org/10.1016/j.cpc.2021.108171}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.26872465
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.022820853
estimated relative force accuracy = 6.872432e-05
using double precision FFTW3
3d grid and FFT values/proc = 4312 960
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
Current simulation parameters: initial step = 100, integration timestep = 2
Updating atomic parameters (masses, charges, etc).
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
SHAKE stats (type/ave/delta/count) on step 100
Bond: 4 1.11098 8.97155e-05 9
Bond: 6 0.996996 1.00568e-05 6
Bond: 8 1.08 6.02345e-06 7
Bond: 10 1.111 1.84253e-05 8
Bond: 12 1.08 7.2713e-06 9
Bond: 14 0.959996 0 1
Bond: 18 0.957198 3.36079e-05 1280
Angle: 31 104.52 0.0030599 640
Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.22 | 16.41 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657
120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812
130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031591
140 253.85111 -5452.1837 -6473.4521 1021.2684 -6609.4826 26.071651 0.30585517
150 261.31816 -5490.4726 -6541.7816 1051.3091 -6646.6075 16.258823 6.9051008
160 255.7352 -5521.5941 -6550.4423 1028.8483 -6658.1373 19.717399 12.339679
170 253.42527 -5540.0942 -6559.6494 1019.5552 -6656.6678 23.293812 10.290217
180 248.51161 -5550.3254 -6550.1125 999.78704 -6661.4235 26.200127 3.4336036
190 250.80862 -5555.2555 -6564.2836 1009.0281 -6666.164 25.53634 3.3494286
SHAKE stats (type/ave/delta/count) on step 200
Bond: 4 1.111 1.81266e-06 9
Bond: 6 0.997 7.79424e-07 6
Bond: 8 1.08 1.08903e-06 7
Bond: 10 1.111 2.96503e-07 8
Bond: 12 1.08 4.69038e-07 9
Bond: 14 0.960001 0 1
Bond: 18 0.957201 3.76471e-06 1280
Angle: 31 104.52 0.000411055 640
200 251.50475 -5557.4252 -6569.2539 1011.8288 -6674.0846 24.804906 7.1387572
Saving collective variables state to "out.colvars.state".
Loop time of 0.238087 on 4 procs for 100 steps with 2004 atoms
Performance: 72.578 ns/day, 0.331 hours/ns, 420.014 timesteps/s, 841.709 katom-step/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.17913 | 0.18408 | 0.19082 | 1.1 | 77.32
Bond | 0.00019617 | 0.00044139 | 0.00071286 | 0.0 | 0.19
Kspace | 0.016186 | 0.022449 | 0.02737 | 3.0 | 9.43
Neigh | 0.018728 | 0.018753 | 0.018777 | 0.0 | 7.88
Comm | 0.0052171 | 0.0055397 | 0.0058422 | 0.3 | 2.33
Output | 0.00012326 | 0.00014453 | 0.00020506 | 0.0 | 0.06
Modify | 0.0062505 | 0.0062725 | 0.0062944 | 0.0 | 2.63
Other | | 0.0004069 | | | 0.17
Nlocal: 501 ave 513 max 481 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 6556.5 ave 6608 max 6514 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 177021 ave 182259 max 172089 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 708083
Ave neighs/atom = 353.33483
Ave special neighs/atom = 2.3403194
Neighbor list builds = 7
Dangerous builds = 0
fix 2 all colvars peptide.colvars input out.colvars.state output out2
----------------------------------------------------------------------
Initializing the collective variables module, version 2024-06-04.
Please cite Fiorin et al, Mol Phys 2013:
https://doi.org/10.1080/00268976.2013.813594
as well as all other papers listed below for individual features used.
Please cite Fiorin et al, Mol Phys 2013:
https://doi.org/10.1080/00268976.2013.813594
as well as all other papers listed below for individual features used.
Please cite Fiorin et al, Mol Phys 2013:
https://doi.org/10.1080/00268976.2013.813594
as well as all other papers listed below for individual features used.
This version was built with the C++11 standard or higher.
Summary of compile-time features available in this build:
- SMP parallelism: enabled (num. threads = 1)
- Lepton custom functions: available
- Tcl interpreter: not available
Using LAMMPS interface, version "2024-07-05".
Setting initial step number from MD engine: 200
run 100
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.26872465
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.022820853
estimated relative force accuracy = 6.872432e-05
using double precision FFTW3
3d grid and FFT values/proc = 4312 960
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
Will read input state from file "out.colvars.state"----------------------------------------------------------------------
Reading new configuration from file "peptide.colvars":
# units = "" [default]
# smp = on [default]
# colvarsTrajFrequency = 1
# colvarsRestartFrequency = 1000
# scriptedColvarForces = off [default]
# scriptingAfterBiases = off [default]
----------------------------------------------------------------------
Initializing a new collective variable.
# name = "one"
Initializing a new "distance" component.
# name = "" [default]
# componentCoeff = 1 [default]
# componentExp = 1 [default]
# period = 0 [default]
# wrapAround = 0 [default]
# forceNoPBC = off [default]
# scalable = on [default]
Initializing atom group "group1".
# name = "" [default]
# centerToOrigin = off [default]
# centerToReference = off [default]
# rotateToReference = off [default]
# atomsOfGroup = "" [default]
# indexGroup = "" [default]
# psfSegID = [default]
# atomsFile = "" [default]
# dummyAtom = ( 0 , 0 , 0 ) [default]
# enableFitGradients = on [default]
# printAtomIDs = off [default]
Atom group "group1" defined with 4 atoms requested.
Initializing atom group "group2".
# name = "" [default]
# centerToOrigin = off [default]
# centerToReference = off [default]
# rotateToReference = off [default]
# atomsOfGroup = "" [default]
# indexGroup = "" [default]
# psfSegID = [default]
# atomsFile = "" [default]
# dummyAtom = ( 0 , 0 , 0 ) [default]
# enableFitGradients = on [default]
# printAtomIDs = off [default]
Atom group "group2" defined with 1 atoms requested.
# oneSiteSystemForce = off [default]
# oneSiteTotalForce = off [default]
All components initialized.
# timeStepFactor = 1 [default]
# width = 1 [default]
# lowerBoundary = 0 [default]
# upperBoundary = 1 [default]
# hardLowerBoundary = on [default]
# hardUpperBoundary = off [default]
# expandBoundaries = off [default]
# extendedLagrangian = off [default]
# outputValue = on [default]
# outputVelocity = off [default]
# outputTotalForce = off [default]
# outputAppliedForce = off [default]
# subtractAppliedForce = off [default]
# runAve = off [default]
# corrFunc = off [default]
----------------------------------------------------------------------
Initializing a new collective variable.
# name = "two"
Initializing a new "distance" component.
# name = "" [default]
# componentCoeff = 1 [default]
# componentExp = 1 [default]
# period = 0 [default]
# wrapAround = 0 [default]
# forceNoPBC = off [default]
# scalable = on [default]
Initializing atom group "group1".
# name = "" [default]
# centerToOrigin = off [default]
# centerToReference = off [default]
# rotateToReference = off [default]
# atomsOfGroup = "" [default]
# indexGroup = "" [default]
# psfSegID = [default]
# atomsFile = "" [default]
# dummyAtom = ( 0 , 0 , 0 ) [default]
# enableFitGradients = on [default]
# printAtomIDs = off [default]
Atom group "group1" defined with 4 atoms requested.
Initializing atom group "group2".
# name = "" [default]
# centerToOrigin = off [default]
# centerToReference = off [default]
# rotateToReference = off [default]
# atomsOfGroup = "" [default]
# indexGroup = "" [default]
# psfSegID = [default]
# atomsFile = "" [default]
# dummyAtom = ( 0 , 0 , 0 ) [default]
# enableFitGradients = on [default]
# printAtomIDs = off [default]
Atom group "group2" defined with 1 atoms requested.
# oneSiteSystemForce = off [default]
# oneSiteTotalForce = off [default]
All components initialized.
# timeStepFactor = 1 [default]
# width = 1 [default]
# lowerBoundary = 0 [default]
# upperBoundary = 1 [default]
# hardLowerBoundary = on [default]
# hardUpperBoundary = off [default]
# expandBoundaries = off [default]
# extendedLagrangian = off [default]
# outputValue = on [default]
# outputVelocity = off [default]
# outputTotalForce = off [default]
# outputAppliedForce = off [default]
# subtractAppliedForce = off [default]
# runAve = off [default]
# corrFunc = off [default]
----------------------------------------------------------------------
Collective variables initialized, 2 in total.
----------------------------------------------------------------------
Initializing a new "harmonic" instance.
# name = "h_pot"
# colvars = { one, two }
# stepZeroData = off [default]
# outputEnergy = off [default]
# outputFreq = 1000 [default]
# timeStepFactor = 1 [default]
# writeTISamples = off [default]
# writeTIPMF = off [default]
# centers = { 10, 10 }
# targetCenters = { 10, 10 } [default]
# outputCenters = off [default]
# forceConstant = 100
# decoupling = off [default]
# targetForceConstant = -1 [default]
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
The force constant for colvar "two" will be rescaled to 100 according to the specified width (1).
----------------------------------------------------------------------
Collective variables biases initialized, 1 in total.
----------------------------------------------------------------------
Collective variables module (re)initialized.
----------------------------------------------------------------------
Current simulation parameters: initial step = 200, integration timestep = 2
Updating atomic parameters (masses, charges, etc).
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
----------------------------------------------------------------------
Loading state from text file "out.colvars.state".
Restarting collective variable "one" from value: 10.0128
Restarting collective variable "two" from value: 9.62236
Restarted harmonic bias "h_pot" with step number 200.
----------------------------------------------------------------------
The final output state file will be "out2.colvars.state".
SHAKE stats (type/ave/delta/count) on step 200
Bond: 4 1.111 1.81266e-06 9
Bond: 6 0.997 7.79424e-07 6
Bond: 8 1.08 1.08903e-06 7
Bond: 10 1.111 2.96503e-07 8
Bond: 12 1.08 4.69038e-07 9
Bond: 14 0.960001 0 1
Bond: 18 0.957201 3.76471e-06 1280
Angle: 31 104.52 0.000411055 640
Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.22 | 16.41 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
200 251.50475 -5557.4252 -6569.2539 1011.8288 -6674.0846 24.804906 7.1387572
210 253.15302 -5538.5615 -6557.0215 1018.4599 -6672.0498 37.676621 0.61219488
220 245.19621 -5522.5191 -6508.9679 986.44887 -6628.1899 36.657688 0.048643387
230 258.69885 -5495.7275 -6536.4989 1040.7713 -6658.2886 34.857911 0.22092559
240 260.79633 -5469.8678 -6519.0775 1049.2097 -6624.18 31.576952 3.7574815
250 269.07527 -5438.3946 -6520.9113 1082.5167 -6616.4382 25.447675 8.6600023
260 266.01046 -5397.3485 -6467.5352 1070.1867 -6580.2896 26.871919 8.3323104
270 272.81307 -5350.8819 -6448.4362 1097.5543 -6563.8228 23.114196 10.973132
280 279.42265 -5307.9799 -6432.1251 1124.1452 -6557.3368 33.644022 8.5490489
290 286.85168 -5260.841 -6414.874 1154.033 -6515.6797 28.574838 5.9100102
SHAKE stats (type/ave/delta/count) on step 300
Bond: 4 1.111 1.79793e-05 9
Bond: 6 0.997005 1.02512e-05 6
Bond: 8 1.08 1.85103e-05 7
Bond: 10 1.111 9.9884e-06 8
Bond: 12 1.08 8.84114e-06 9
Bond: 14 0.960008 0 1
Bond: 18 0.957203 1.8445e-05 1280
Angle: 31 104.52 0.00168383 640
300 291.52793 -5216.288 -6389.1341 1172.846 -6503.1275 27.88915 2.2482428
Saving collective variables state to "out2.colvars.state".
Loop time of 0.245933 on 4 procs for 100 steps with 2004 atoms
Performance: 70.263 ns/day, 0.342 hours/ns, 406.614 timesteps/s, 814.854 katom-step/s
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.17862 | 0.18666 | 0.19126 | 1.2 | 75.90
Bond | 0.00021974 | 0.00048505 | 0.00077708 | 0.0 | 0.20
Kspace | 0.018338 | 0.02317 | 0.031148 | 3.4 | 9.42
Neigh | 0.022128 | 0.022183 | 0.022222 | 0.0 | 9.02
Comm | 0.0059137 | 0.0060593 | 0.0064247 | 0.3 | 2.46
Output | 0.00014648 | 0.00015946 | 0.00019596 | 0.0 | 0.06
Modify | 0.0067012 | 0.00674 | 0.0067814 | 0.0 | 2.74
Other | | 0.0004738 | | | 0.19
Nlocal: 501 ave 513 max 472 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost: 6612.75 ave 6681 max 6561 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Neighs: 177038 ave 180136 max 170218 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Total # of neighbors = 708152
Ave neighs/atom = 353.36926
Ave special neighs/atom = 2.3403194
Neighbor list builds = 8
Dangerous builds = 0
Total wall time: 0:00:00

344
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars2.g++.1 Normal file
View File

@ -0,0 +1,344 @@
LAMMPS (27 Jun 2024)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
Reading data file ...
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
1 by 1 by 1 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
1 by 1 by 1 MPI processor grid
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.012 seconds
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
group peptide type <= 12
84 atoms in group peptide
group one id 2 4 5 6
4 atoms in group one
group two id 80 82 83 84
4 atoms in group two
group ref id 37
1 atoms in group ref
group colvar union one two ref
9 atoms in group colvar
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
shell "rm -f peptide2.colvars.*"
fix 2 all colvars peptide.colvars2 output peptide2
----------------------------------------------------------------------
Initializing the collective variables module, version 2024-06-04.
Please cite Fiorin et al, Mol Phys 2013:
https://doi.org/10.1080/00268976.2013.813594
as well as all other papers listed below for individual features used.
Please cite Fiorin et al, Mol Phys 2013:
https://doi.org/10.1080/00268976.2013.813594
as well as all other papers listed below for individual features used.
Please cite Fiorin et al, Mol Phys 2013:
https://doi.org/10.1080/00268976.2013.813594
as well as all other papers listed below for individual features used.
This version was built with the C++11 standard or higher.
Summary of compile-time features available in this build:
- SMP parallelism: enabled (num. threads = 1)
- Lepton custom functions: available
- Tcl interpreter: not available
Using LAMMPS interface, version "2024-07-05".
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
Finding SHAKE clusters ...
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
find clusters CPU = 0.000 seconds
#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
thermo_style custom step temp etotal pe ke epair ebond f_2
thermo 10
run 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
@Article{Gissinger24,
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
journal = {J. Phys. Chem. B},
year = 2024,
volume = 128,
number = 13,
pages = {3282–-3297}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.26872465
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.022820853
estimated relative force accuracy = 6.872432e-05
using double precision FFTW3
3d grid and FFT values/proc = 10648 3375
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 5 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
----------------------------------------------------------------------
Reading new configuration from file "peptide.colvars2":
# units = "" [default]
# smp = on [default]
# colvarsTrajFrequency = 1
# colvarsRestartFrequency = 1000
# scriptedColvarForces = off [default]
# scriptingAfterBiases = off [default]
----------------------------------------------------------------------
Initializing a new collective variable.
# name = "one"
Initializing a new "distance" component.
# name = "" [default]
# componentCoeff = 1 [default]
# componentExp = 1 [default]
# period = 0 [default]
# wrapAround = 0 [default]
# forceNoPBC = off [default]
# scalable = on [default]
Initializing atom group "group1".
# name = "" [default]
# centerToOrigin = off [default]
# centerToReference = off [default]
# rotateToReference = off [default]
# atomsOfGroup = "" [default]
# indexGroup = "" [default]
# psfSegID = [default]
# atomsFile = "" [default]
# dummyAtom = ( 0 , 0 , 0 ) [default]
# enableFitGradients = on [default]
# printAtomIDs = off [default]
Atom group "group1" defined with 4 atoms requested.
Initializing atom group "group2".
# name = "" [default]
# centerToOrigin = off [default]
# centerToReference = off [default]
# rotateToReference = off [default]
# atomsOfGroup = "" [default]
# indexGroup = "" [default]
# psfSegID = [default]
# atomsFile = "" [default]
# dummyAtom = ( 0 , 0 , 0 ) [default]
# enableFitGradients = on [default]
# printAtomIDs = off [default]
Atom group "group2" defined with 4 atoms requested.
# oneSiteSystemForce = off [default]
# oneSiteTotalForce = off [default]
All components initialized.
# timeStepFactor = 1 [default]
# width = 1 [default]
# lowerBoundary = 0 [default]
# upperBoundary = 1 [default]
# hardLowerBoundary = on [default]
# hardUpperBoundary = off [default]
# expandBoundaries = off [default]
# extendedLagrangian = off [default]
# outputValue = on [default]
# outputVelocity = off [default]
# outputTotalForce = off [default]
# outputAppliedForce = off [default]
# subtractAppliedForce = off [default]
# runAve = off [default]
# corrFunc = off [default]
----------------------------------------------------------------------
Collective variables initialized, 1 in total.
----------------------------------------------------------------------
Initializing a new "harmonic" instance.
# name = "h_pot"
# colvars = { one }
# stepZeroData = off [default]
# outputEnergy = off [default]
# outputFreq = 1000 [default]
# timeStepFactor = 1 [default]
# writeTISamples = off [default]
# writeTIPMF = off [default]
# centers = { 10 }
# targetCenters = { 10 } [default]
# outputCenters = off [default]
# forceConstant = 100
# decoupling = off [default]
# targetForceConstant = -1 [default]
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
----------------------------------------------------------------------
Collective variables biases initialized, 1 in total.
----------------------------------------------------------------------
Collective variables module (re)initialized.
----------------------------------------------------------------------
Current simulation parameters: initial step = 0, integration timestep = 2
Updating atomic parameters (masses, charges, etc).
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 15.035, total charge = 0.16.
The final output state file will be "peptide2.colvars.state".
Synchronizing (emptying the buffer of) trajectory file "peptide2.colvars.traj".
SHAKE stats (type/ave/delta/count) on step 0
Bond: 4 1.111 1.44264e-05 9
Bond: 6 0.996998 7.26967e-06 6
Bond: 8 1.08 1.32536e-05 7
Bond: 10 1.111 1.22749e-05 8
Bond: 12 1.08 1.11767e-05 9
Bond: 14 0.96 0 1
Bond: 18 0.957206 4.37979e-05 1280
Angle: 31 104.519 0.00396029 640
Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
SHAKE stats (type/ave/delta/count) on step 100
Bond: 4 1.11096 0.000191462 9
Bond: 6 0.996989 3.55508e-05 6
Bond: 8 1.08 9.0997e-06 7
Bond: 10 1.111 1.58544e-05 8
Bond: 12 1.08 5.80604e-06 9
Bond: 14 0.959997 0 1
Bond: 18 0.957198 2.92445e-05 1280
Angle: 31 104.52 0.00239923 640
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
Saving collective variables state to "peptide2.colvars.state".
Loop time of 0.907882 on 1 procs for 100 steps with 2004 atoms
Performance: 19.033 ns/day, 1.261 hours/ns, 110.146 timesteps/s, 220.734 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.71563 | 0.71563 | 0.71563 | 0.0 | 78.82
Bond | 0.0013267 | 0.0013267 | 0.0013267 | 0.0 | 0.15
Kspace | 0.042157 | 0.042157 | 0.042157 | 0.0 | 4.64
Neigh | 0.13452 | 0.13452 | 0.13452 | 0.0 | 14.82
Comm | 0.0034995 | 0.0034995 | 0.0034995 | 0.0 | 0.39
Output | 0.00014584 | 0.00014584 | 0.00014584 | 0.0 | 0.02
Modify | 0.010115 | 0.010115 | 0.010115 | 0.0 | 1.11
Other | | 0.0004888 | | | 0.05
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11143 ave 11143 max 11143 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 708234 ave 708234 max 708234 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708234
Ave neighs/atom = 353.41018
Ave special neighs/atom = 2.3403194
Neighbor list builds = 13
Dangerous builds = 1
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Colvars module (Fiorin2013, plus other works listed for specific features)
% Colvars module:
% Colvars-LAMMPS interface:
% Harmonic colvar bias implementation:
% Optimal rotation via flexible fitting:
% distance colvar component:
@article{Fiorin2013,
author = {Fiorin, Giacomo and Klein, Michael L.{} and H\'enin, J\'er\^ome},
title = {Using collective variables to drive molecular dynamics simulations},
journal = {Mol. Phys.},
year = {2013},
volume = {111},
number = {22-23},
pages = {3345--3362},
publisher = {Taylor & Francis},
doi = {10.1080/00268976.2013.813594},
url = {https://doi.org/10.1080/00268976.2013.813594}
}
% LAMMPS engine:
@article{Thompson2022,
title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and {in't Veld}, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.},
journal = {Comp. Phys. Comm.},
volume = {271},
pages = {108171},
year = {2022},
doi = {10.1016/j.cpc.2021.108171},
url = {https://doi.org/10.1016/j.cpc.2021.108171}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Total wall time: 0:00:00

344
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars2.g++.4 Normal file
View File

@ -0,0 +1,344 @@
LAMMPS (27 Jun 2024)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
Reading data file ...
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
1 by 2 by 2 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
1 by 2 by 2 MPI processor grid
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.011 seconds
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
group peptide type <= 12
84 atoms in group peptide
group one id 2 4 5 6
4 atoms in group one
group two id 80 82 83 84
4 atoms in group two
group ref id 37
1 atoms in group ref
group colvar union one two ref
9 atoms in group colvar
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
shell "rm -f peptide2.colvars.*"
fix 2 all colvars peptide.colvars2 output peptide2
----------------------------------------------------------------------
Initializing the collective variables module, version 2024-06-04.
Please cite Fiorin et al, Mol Phys 2013:
https://doi.org/10.1080/00268976.2013.813594
as well as all other papers listed below for individual features used.
Please cite Fiorin et al, Mol Phys 2013:
https://doi.org/10.1080/00268976.2013.813594
as well as all other papers listed below for individual features used.
Please cite Fiorin et al, Mol Phys 2013:
https://doi.org/10.1080/00268976.2013.813594
as well as all other papers listed below for individual features used.
This version was built with the C++11 standard or higher.
Summary of compile-time features available in this build:
- SMP parallelism: enabled (num. threads = 1)
- Lepton custom functions: available
- Tcl interpreter: not available
Using LAMMPS interface, version "2024-07-05".
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
Finding SHAKE clusters ...
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
find clusters CPU = 0.000 seconds
#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
thermo_style custom step temp etotal pe ke epair ebond f_2
thermo 10
run 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
@Article{Gissinger24,
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
journal = {J. Phys. Chem. B},
year = 2024,
volume = 128,
number = 13,
pages = {3282–-3297}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.26872465
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.022820853
estimated relative force accuracy = 6.872432e-05
using double precision FFTW3
3d grid and FFT values/proc = 4312 960
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 5 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
----------------------------------------------------------------------
Reading new configuration from file "peptide.colvars2":
# units = "" [default]
# smp = on [default]
# colvarsTrajFrequency = 1
# colvarsRestartFrequency = 1000
# scriptedColvarForces = off [default]
# scriptingAfterBiases = off [default]
----------------------------------------------------------------------
Initializing a new collective variable.
# name = "one"
Initializing a new "distance" component.
# name = "" [default]
# componentCoeff = 1 [default]
# componentExp = 1 [default]
# period = 0 [default]
# wrapAround = 0 [default]
# forceNoPBC = off [default]
# scalable = on [default]
Initializing atom group "group1".
# name = "" [default]
# centerToOrigin = off [default]
# centerToReference = off [default]
# rotateToReference = off [default]
# atomsOfGroup = "" [default]
# indexGroup = "" [default]
# psfSegID = [default]
# atomsFile = "" [default]
# dummyAtom = ( 0 , 0 , 0 ) [default]
# enableFitGradients = on [default]
# printAtomIDs = off [default]
Atom group "group1" defined with 4 atoms requested.
Initializing atom group "group2".
# name = "" [default]
# centerToOrigin = off [default]
# centerToReference = off [default]
# rotateToReference = off [default]
# atomsOfGroup = "" [default]
# indexGroup = "" [default]
# psfSegID = [default]
# atomsFile = "" [default]
# dummyAtom = ( 0 , 0 , 0 ) [default]
# enableFitGradients = on [default]
# printAtomIDs = off [default]
Atom group "group2" defined with 4 atoms requested.
# oneSiteSystemForce = off [default]
# oneSiteTotalForce = off [default]
All components initialized.
# timeStepFactor = 1 [default]
# width = 1 [default]
# lowerBoundary = 0 [default]
# upperBoundary = 1 [default]
# hardLowerBoundary = on [default]
# hardUpperBoundary = off [default]
# expandBoundaries = off [default]
# extendedLagrangian = off [default]
# outputValue = on [default]
# outputVelocity = off [default]
# outputTotalForce = off [default]
# outputAppliedForce = off [default]
# subtractAppliedForce = off [default]
# runAve = off [default]
# corrFunc = off [default]
----------------------------------------------------------------------
Collective variables initialized, 1 in total.
----------------------------------------------------------------------
Initializing a new "harmonic" instance.
# name = "h_pot"
# colvars = { one }
# stepZeroData = off [default]
# outputEnergy = off [default]
# outputFreq = 1000 [default]
# timeStepFactor = 1 [default]
# writeTISamples = off [default]
# writeTIPMF = off [default]
# centers = { 10 }
# targetCenters = { 10 } [default]
# outputCenters = off [default]
# forceConstant = 100
# decoupling = off [default]
# targetForceConstant = -1 [default]
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
----------------------------------------------------------------------
Collective variables biases initialized, 1 in total.
----------------------------------------------------------------------
Collective variables module (re)initialized.
----------------------------------------------------------------------
Current simulation parameters: initial step = 0, integration timestep = 2
Updating atomic parameters (masses, charges, etc).
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 15.035, total charge = 0.16.
The final output state file will be "peptide2.colvars.state".
Synchronizing (emptying the buffer of) trajectory file "peptide2.colvars.traj".
SHAKE stats (type/ave/delta/count) on step 0
Bond: 4 1.111 1.44264e-05 9
Bond: 6 0.996998 7.26967e-06 6
Bond: 8 1.08 1.32536e-05 7
Bond: 10 1.111 1.22749e-05 8
Bond: 12 1.08 1.11767e-05 9
Bond: 14 0.96 0 1
Bond: 18 0.957206 4.37979e-05 1280
Angle: 31 104.519 0.00396029 640
Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.22 | 16.41 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
SHAKE stats (type/ave/delta/count) on step 100
Bond: 4 1.11096 0.000191462 9
Bond: 6 0.996989 3.55508e-05 6
Bond: 8 1.08 9.0997e-06 7
Bond: 10 1.111 1.58544e-05 8
Bond: 12 1.08 5.80604e-06 9
Bond: 14 0.959997 0 1
Bond: 18 0.957198 2.92445e-05 1280
Angle: 31 104.52 0.00239923 640
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
Saving collective variables state to "peptide2.colvars.state".
Loop time of 0.253421 on 4 procs for 100 steps with 2004 atoms
Performance: 68.187 ns/day, 0.352 hours/ns, 394.600 timesteps/s, 790.779 katom-step/s
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.1771 | 0.18185 | 0.18625 | 0.8 | 71.76
Bond | 0.00028771 | 0.00056007 | 0.00087366 | 0.0 | 0.22
Kspace | 0.017434 | 0.021451 | 0.026345 | 2.4 | 8.46
Neigh | 0.035481 | 0.035495 | 0.035512 | 0.0 | 14.01
Comm | 0.0064003 | 0.0065098 | 0.0065994 | 0.1 | 2.57
Output | 0.00012417 | 0.00013888 | 0.00018109 | 0.0 | 0.05
Modify | 0.0069389 | 0.0069521 | 0.0069617 | 0.0 | 2.74
Other | | 0.0004667 | | | 0.18
Nlocal: 501 ave 513 max 494 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Nghost: 6572.5 ave 6593 max 6548 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 177058 ave 181778 max 174301 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 708234
Ave neighs/atom = 353.41018
Ave special neighs/atom = 2.3403194
Neighbor list builds = 13
Dangerous builds = 1
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Colvars module (Fiorin2013, plus other works listed for specific features)
% Colvars module:
% Colvars-LAMMPS interface:
% Harmonic colvar bias implementation:
% Optimal rotation via flexible fitting:
% distance colvar component:
@article{Fiorin2013,
author = {Fiorin, Giacomo and Klein, Michael L.{} and H\'enin, J\'er\^ome},
title = {Using collective variables to drive molecular dynamics simulations},
journal = {Mol. Phys.},
year = {2013},
volume = {111},
number = {22-23},
pages = {3345--3362},
publisher = {Taylor & Francis},
doi = {10.1080/00268976.2013.813594},
url = {https://doi.org/10.1080/00268976.2013.813594}
}
% LAMMPS engine:
@article{Thompson2022,
title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and {in't Veld}, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.},
journal = {Comp. Phys. Comm.},
volume = {271},
pages = {108171},
year = {2022},
doi = {10.1016/j.cpc.2021.108171},
url = {https://doi.org/10.1016/j.cpc.2021.108171}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Total wall time: 0:00:00

194
examples/PACKAGES/colvars/log.5Aug24.peptide-spring.g++.1 Normal file
View File

@ -0,0 +1,194 @@
LAMMPS (27 Jun 2024)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
Reading data file ...
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
1 by 1 by 1 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
1 by 1 by 1 MPI processor grid
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.012 seconds
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
group peptide type <= 12
84 atoms in group peptide
group one id 2 4 5 6
4 atoms in group one
group two id 80 82 83 84
4 atoms in group two
group ref id 37
1 atoms in group ref
group colvar union one two ref
9 atoms in group colvar
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0
fix 2a ref setforce 0.0 0.0 0.0
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
Finding SHAKE clusters ...
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
find clusters CPU = 0.000 seconds
#dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
variable sp equal f_3a+f_3b
thermo_style custom step temp etotal pe ke epair ebond v_sp
thermo 10
run 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
@Article{Gissinger24,
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
journal = {J. Phys. Chem. B},
year = 2024,
volume = 128,
number = 13,
pages = {3282–-3297}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.26872465
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.022820853
estimated relative force accuracy = 6.872432e-05
using double precision FFTW3
3d grid and FFT values/proc = 10648 3375
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 5 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
SHAKE stats (type/ave/delta/count) on step 0
Bond: 4 1.111 1.44264e-05 9
Bond: 6 0.996998 7.26967e-06 6
Bond: 8 1.08 1.32536e-05 7
Bond: 10 1.111 1.22749e-05 8
Bond: 12 1.08 1.11767e-05 9
Bond: 14 0.96 0 1
Bond: 18 0.957206 4.37979e-05 1280
Angle: 31 104.519 0.00396029 640
Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond v_sp
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
SHAKE stats (type/ave/delta/count) on step 100
Bond: 4 1.11098 8.97155e-05 9
Bond: 6 0.996996 1.00568e-05 6
Bond: 8 1.08 6.02345e-06 7
Bond: 10 1.111 1.84253e-05 8
Bond: 12 1.08 7.2713e-06 9
Bond: 14 0.959996 0 1
Bond: 18 0.957198 3.36079e-05 1280
Angle: 31 104.52 0.0030599 640
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
Loop time of 0.893963 on 1 procs for 100 steps with 2004 atoms
Performance: 19.330 ns/day, 1.242 hours/ns, 111.861 timesteps/s, 224.170 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.7114 | 0.7114 | 0.7114 | 0.0 | 79.58
Bond | 0.0012663 | 0.0012663 | 0.0012663 | 0.0 | 0.14
Kspace | 0.041962 | 0.041962 | 0.041962 | 0.0 | 4.69
Neigh | 0.12542 | 0.12542 | 0.12542 | 0.0 | 14.03
Comm | 0.0033466 | 0.0033466 | 0.0033466 | 0.0 | 0.37
Output | 0.00017765 | 0.00017765 | 0.00017765 | 0.0 | 0.02
Modify | 0.0098927 | 0.0098927 | 0.0098927 | 0.0 | 1.11
Other | | 0.0005014 | | | 0.06
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11124 ave 11124 max 11124 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 708237 ave 708237 max 708237 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708237
Ave neighs/atom = 353.41168
Ave special neighs/atom = 2.3403194
Neighbor list builds = 12
Dangerous builds = 2
Total wall time: 0:00:00

194
examples/PACKAGES/colvars/log.5Aug24.peptide-spring.g++.4 Normal file
View File

@ -0,0 +1,194 @@
LAMMPS (27 Jun 2024)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
Reading data file ...
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
1 by 2 by 2 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
1 by 2 by 2 MPI processor grid
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.010 seconds
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
group peptide type <= 12
84 atoms in group peptide
group one id 2 4 5 6
4 atoms in group one
group two id 80 82 83 84
4 atoms in group two
group ref id 37
1 atoms in group ref
group colvar union one two ref
9 atoms in group colvar
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0
fix 2a ref setforce 0.0 0.0 0.0
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
Finding SHAKE clusters ...
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
find clusters CPU = 0.000 seconds
#dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
variable sp equal f_3a+f_3b
thermo_style custom step temp etotal pe ke epair ebond v_sp
thermo 10
run 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
@Article{Gissinger24,
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
journal = {J. Phys. Chem. B},
year = 2024,
volume = 128,
number = 13,
pages = {3282–-3297}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.26872465
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.022820853
estimated relative force accuracy = 6.872432e-05
using double precision FFTW3
3d grid and FFT values/proc = 4312 960
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 5 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
SHAKE stats (type/ave/delta/count) on step 0
Bond: 4 1.111 1.44264e-05 9
Bond: 6 0.996998 7.26967e-06 6
Bond: 8 1.08 1.32536e-05 7
Bond: 10 1.111 1.22749e-05 8
Bond: 12 1.08 1.11767e-05 9
Bond: 14 0.96 0 1
Bond: 18 0.957206 4.37979e-05 1280
Angle: 31 104.519 0.00396029 640
Per MPI rank memory allocation (min/avg/max) = 16.01 | 16.22 | 16.41 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond v_sp
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
SHAKE stats (type/ave/delta/count) on step 100
Bond: 4 1.11098 8.97155e-05 9
Bond: 6 0.996996 1.00568e-05 6
Bond: 8 1.08 6.02345e-06 7
Bond: 10 1.111 1.84253e-05 8
Bond: 12 1.08 7.2713e-06 9
Bond: 14 0.959996 0 1
Bond: 18 0.957198 3.36079e-05 1280
Angle: 31 104.52 0.0030599 640
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
Loop time of 0.247541 on 4 procs for 100 steps with 2004 atoms
Performance: 69.806 ns/day, 0.344 hours/ns, 403.973 timesteps/s, 809.561 katom-step/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.17778 | 0.18129 | 0.18529 | 0.8 | 73.24
Bond | 0.00024025 | 0.00049912 | 0.00080235 | 0.0 | 0.20
Kspace | 0.016204 | 0.0204 | 0.023648 | 2.3 | 8.24
Neigh | 0.032425 | 0.032462 | 0.032496 | 0.0 | 13.11
Comm | 0.0063955 | 0.0065509 | 0.0067449 | 0.2 | 2.65
Output | 0.0001675 | 0.00018071 | 0.00021385 | 0.0 | 0.07
Modify | 0.0057027 | 0.0057304 | 0.0057568 | 0.0 | 2.31
Other | | 0.0004289 | | | 0.17
Nlocal: 501 ave 513 max 489 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 6563.25 ave 6596 max 6519 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 177059 ave 181742 max 172942 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 708237
Ave neighs/atom = 353.41168
Ave special neighs/atom = 2.3403194
Neighbor list builds = 12
Dangerous builds = 2
Total wall time: 0:00:00

189
examples/PACKAGES/colvars/log.5Aug24.peptide-spring2.g++.1 Normal file
View File

@ -0,0 +1,189 @@
LAMMPS (27 Jun 2024)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
Reading data file ...
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
1 by 1 by 1 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
1 by 1 by 1 MPI processor grid
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.012 seconds
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
group peptide type <= 12
84 atoms in group peptide
group one id 2 4 5 6
4 atoms in group one
group two id 80 82 83 84
4 atoms in group two
group ref id 37
1 atoms in group ref
group colvar union one two ref
9 atoms in group colvar
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
Finding SHAKE clusters ...
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
find clusters CPU = 0.000 seconds
#dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
thermo_style custom step temp etotal pe ke epair ebond f_3
thermo 10
run 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
@Article{Gissinger24,
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
journal = {J. Phys. Chem. B},
year = 2024,
volume = 128,
number = 13,
pages = {3282–-3297}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.26872465
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.022820853
estimated relative force accuracy = 6.872432e-05
using double precision FFTW3
3d grid and FFT values/proc = 10648 3375
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 5 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
SHAKE stats (type/ave/delta/count) on step 0
Bond: 4 1.111 1.44264e-05 9
Bond: 6 0.996998 7.26967e-06 6
Bond: 8 1.08 1.32536e-05 7
Bond: 10 1.111 1.22749e-05 8
Bond: 12 1.08 1.11767e-05 9
Bond: 14 0.96 0 1
Bond: 18 0.957206 4.37979e-05 1280
Angle: 31 104.519 0.00396029 640
Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_3
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
SHAKE stats (type/ave/delta/count) on step 100
Bond: 4 1.11096 0.000191462 9
Bond: 6 0.996989 3.55508e-05 6
Bond: 8 1.08 9.0997e-06 7
Bond: 10 1.111 1.58544e-05 8
Bond: 12 1.08 5.80604e-06 9
Bond: 14 0.959997 0 1
Bond: 18 0.957198 2.92445e-05 1280
Angle: 31 104.52 0.00239923 640
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
Loop time of 0.910778 on 1 procs for 100 steps with 2004 atoms
Performance: 18.973 ns/day, 1.265 hours/ns, 109.796 timesteps/s, 220.032 katom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.71746 | 0.71746 | 0.71746 | 0.0 | 78.77
Bond | 0.0012756 | 0.0012756 | 0.0012756 | 0.0 | 0.14
Kspace | 0.042462 | 0.042462 | 0.042462 | 0.0 | 4.66
Neigh | 0.13497 | 0.13497 | 0.13497 | 0.0 | 14.82
Comm | 0.0036247 | 0.0036247 | 0.0036247 | 0.0 | 0.40
Output | 0.00016145 | 0.00016145 | 0.00016145 | 0.0 | 0.02
Modify | 0.010258 | 0.010258 | 0.010258 | 0.0 | 1.13
Other | | 0.0005695 | | | 0.06
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11143 ave 11143 max 11143 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 708234 ave 708234 max 708234 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708234
Ave neighs/atom = 353.41018
Ave special neighs/atom = 2.3403194
Neighbor list builds = 13
Dangerous builds = 1
Total wall time: 0:00:00

189
examples/PACKAGES/colvars/log.5Aug24.peptide-spring2.g++.4 Normal file
View File

@ -0,0 +1,189 @@
LAMMPS (27 Jun 2024)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
Reading data file ...
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
1 by 2 by 2 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
1 by 2 by 2 MPI processor grid
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
12 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.011 seconds
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
group peptide type <= 12
84 atoms in group peptide
group one id 2 4 5 6
4 atoms in group one
group two id 80 82 83 84
4 atoms in group two
group ref id 37
1 atoms in group ref
group colvar union one two ref
9 atoms in group colvar
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
Finding SHAKE clusters ...
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
find clusters CPU = 0.000 seconds
#dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz
#dump_modify 1 sort id
thermo_style custom step temp etotal pe ke epair ebond f_3
thermo 10
run 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
@Article{Gissinger24,
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
journal = {J. Phys. Chem. B},
year = 2024,
volume = 128,
number = 13,
pages = {3282–-3297}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.26872465
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.022820853
estimated relative force accuracy = 6.872432e-05
using double precision FFTW3
3d grid and FFT values/proc = 4312 960
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 5 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/charmm/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
SHAKE stats (type/ave/delta/count) on step 0
Bond: 4 1.111 1.44264e-05 9
Bond: 6 0.996998 7.26967e-06 6
Bond: 8 1.08 1.32536e-05 7
Bond: 10 1.111 1.22749e-05 8
Bond: 12 1.08 1.11767e-05 9
Bond: 14 0.96 0 1
Bond: 18 0.957206 4.37979e-05 1280
Angle: 31 104.519 0.00396029 640
Per MPI rank memory allocation (min/avg/max) = 16.01 | 16.22 | 16.41 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond f_3
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
SHAKE stats (type/ave/delta/count) on step 100
Bond: 4 1.11096 0.000191462 9
Bond: 6 0.996989 3.55508e-05 6
Bond: 8 1.08 9.0997e-06 7
Bond: 10 1.111 1.58544e-05 8
Bond: 12 1.08 5.80604e-06 9
Bond: 14 0.959997 0 1
Bond: 18 0.957198 2.92445e-05 1280
Angle: 31 104.52 0.00239923 640
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
Loop time of 0.248812 on 4 procs for 100 steps with 2004 atoms
Performance: 69.450 ns/day, 0.346 hours/ns, 401.910 timesteps/s, 805.428 katom-step/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.17522 | 0.18002 | 0.18454 | 1.0 | 72.35
Bond | 0.00020312 | 0.00044793 | 0.00074786 | 0.0 | 0.18
Kspace | 0.016556 | 0.021002 | 0.026079 | 3.0 | 8.44
Neigh | 0.035695 | 0.03571 | 0.03572 | 0.0 | 14.35
Comm | 0.0057324 | 0.0058127 | 0.005874 | 0.1 | 2.34
Output | 0.00013005 | 0.00013946 | 0.00016548 | 0.0 | 0.06
Modify | 0.00526 | 0.0052645 | 0.005272 | 0.0 | 2.12
Other | | 0.0004197 | | | 0.17
Nlocal: 501 ave 513 max 494 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Nghost: 6572.5 ave 6593 max 6548 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 177058 ave 181778 max 174301 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 708234
Ave neighs/atom = 353.41018
Ave special neighs/atom = 2.3403194
Neighbor list builds = 13
Dangerous builds = 1
Total wall time: 0:00:00

6
examples/PACKAGES/colvars/out.colvars.state
View File

@ -1,17 +1,17 @@
configuration {
step 200
dt 2.000000e+00
version 2020-07-07
version 2024-06-04
}
colvar {
name one
x 1.00127732034965e+01
x 10.012773203962
}
colvar {
name two
x 9.62235997490241e+00
x 9.6223599748448
}
restraint {

6
examples/PACKAGES/colvars/out.colvars.state.old
View File

@ -1,17 +1,17 @@
configuration {
step 100
dt 2.000000e+00
version 2020-07-07
version 2024-06-04
}
colvar {
name one
x 1.00136989326255e+01
x 10.013698932648
}
colvar {
name two
x 1.00648830006091e+01
x 10.064883000604
}
restraint {

332
examples/PACKAGES/colvars/out.colvars.traj
View File

@ -13,191 +13,191 @@
11 1.01744058364969e+01 8.66916428851601e+00
12 1.01894584969823e+01 8.75011341291751e+00
13 1.02015949657517e+01 8.81261373358815e+00
14 1.02107634786499e+01 8.86010572643564e+00
14 1.02107634786498e+01 8.86010572643564e+00
15 1.02172802335367e+01 8.89996164389908e+00
16 1.02217586687617e+01 8.94046117354318e+00
17 1.02249400729821e+01 8.98764357480963e+00
18 1.02274821194763e+01 9.04385418276306e+00
19 1.02297694921722e+01 9.10767828090644e+00
20 1.02317948794015e+01 9.17521818721732e+00
20 1.02317948794015e+01 9.17521818721733e+00
21 1.02331324174422e+01 9.24256921345538e+00
22 1.02330115052436e+01 9.30670040650459e+00
22 1.02330115052436e+01 9.30670040650458e+00
23 1.02304888847637e+01 9.36477739916766e+00
24 1.02246905091409e+01 9.41471338314027e+00
25 1.02150557312054e+01 9.45578119421866e+00
26 1.02015018849614e+01 9.48855148434622e+00
27 1.01844563445019e+01 9.51414398880334e+00
26 1.02015018849613e+01 9.48855148434622e+00
27 1.01844563445019e+01 9.51414398880333e+00
28 1.01647618536435e+01 9.53348342780342e+00
29 1.01435075836914e+01 9.54736918677922e+00
30 1.01218448127414e+01 9.55679294480281e+00
30 1.01218448127414e+01 9.55679294480282e+00
31 1.01008234685872e+01 9.56289707955055e+00
32 1.00812605992407e+01 9.56689852729787e+00
33 1.00636482078211e+01 9.57008522470066e+00
34 1.00481219532447e+01 9.57404682801174e+00
35 1.00345149123742e+01 9.58097344406653e+00
32 1.00812605992407e+01 9.56689852729789e+00
33 1.00636482078211e+01 9.57008522470067e+00
34 1.00481219532447e+01 9.57404682801176e+00
35 1.00345149123742e+01 9.58097344406654e+00
36 1.00224896192326e+01 9.59352147402459e+00
37 1.00117065902086e+01 9.61412496221624e+00
38 1.00019625883763e+01 9.64369256665448e+00
39 9.99324045988116e+00 9.68100279483232e+00
40 9.98566198277188e+00 9.72340741886406e+00
41 9.97939087537504e+00 9.76737558060000e+00
42 9.97455220189940e+00 9.80830263552738e+00
43 9.97120052013341e+00 9.84185625268822e+00
44 9.96933202180119e+00 9.86623764187619e+00
45 9.96891976615505e+00 9.88235950966856e+00
46 9.96994868341340e+00 9.89287033859050e+00
47 9.97242707411381e+00 9.90111363064262e+00
48 9.97636549450466e+00 9.91016536955268e+00
49 9.98173560597232e+00 9.92197275407224e+00
50 9.98843048433684e+00 9.93674029911159e+00
39 9.99324045988117e+00 9.68100279483232e+00
40 9.98566198277187e+00 9.72340741886405e+00
41 9.97939087537503e+00 9.76737558059998e+00
42 9.97455220189941e+00 9.80830263552736e+00
43 9.97120052013341e+00 9.84185625268820e+00
44 9.96933202180119e+00 9.86623764187617e+00
45 9.96891976615505e+00 9.88235950966853e+00
46 9.96994868341340e+00 9.89287033859049e+00
47 9.97242707411382e+00 9.90111363064261e+00
48 9.97636549450467e+00 9.91016536955268e+00
49 9.98173560597233e+00 9.92197275407223e+00
50 9.98843048433685e+00 9.93674029911158e+00
51 9.99624064138588e+00 9.95286099036568e+00
52 1.00048525916104e+01 9.96759873289121e+00
53 1.00138780764319e+01 9.97821328789638e+00
53 1.00138780764319e+01 9.97821328789637e+00
54 1.00229204333232e+01 9.98289434996108e+00
55 1.00316676518615e+01 9.98113328544968e+00
56 1.00399758142293e+01 9.97358294450079e+00
57 1.00479031641095e+01 9.96154574170506e+00
58 1.00556838347250e+01 9.94624156425743e+00
59 1.00636555959318e+01 9.92816580065099e+00
60 1.00721640105110e+01 9.90692505955277e+00
56 1.00399758142293e+01 9.97358294450078e+00
57 1.00479031641095e+01 9.96154574170507e+00
58 1.00556838347250e+01 9.94624156425742e+00
59 1.00636555959318e+01 9.92816580065100e+00
60 1.00721640105110e+01 9.90692505955279e+00
61 1.00814536313753e+01 9.88155118527262e+00
62 1.00915547252798e+01 9.85098082230735e+00
63 1.01021918256653e+01 9.81456141006142e+00
64 1.01127650365675e+01 9.77251908261309e+00
62 1.00915547252798e+01 9.85098082230737e+00
63 1.01021918256653e+01 9.81456141006145e+00
64 1.01127650365675e+01 9.77251908261310e+00
65 1.01224426616504e+01 9.72626626484817e+00
66 1.01303500341168e+01 9.67844790721581e+00
66 1.01303500341168e+01 9.67844790721582e+00
67 1.01357827497794e+01 9.63264342158540e+00
68 1.01383594707679e+01 9.59267551611127e+00
69 1.01380701059532e+01 9.56168371312923e+00
70 1.01352290156399e+01 9.54132235576289e+00
71 1.01303782422632e+01 9.53145207033862e+00
72 1.01241807468998e+01 9.53052072472080e+00
73 1.01173118912092e+01 9.53632715678295e+00
74 1.01103471939659e+01 9.54668992740772e+00
75 1.01036629090248e+01 9.55984803752009e+00
76 1.00973931139318e+01 9.57467381743772e+00
77 1.00914805900150e+01 9.59078681449290e+00
78 1.00857806923796e+01 9.60849062320413e+00
79 1.00801732463746e+01 9.62847591791803e+00
80 1.00746211947647e+01 9.65137407697197e+00
81 1.00691682828698e+01 9.67731006831009e+00
82 1.00638992393184e+01 9.70564969348618e+00
83 1.00589006124327e+01 9.73510953407921e+00
84 1.00542402131510e+01 9.76420390471647e+00
85 1.00499602946160e+01 9.79180385249033e+00
86 1.00460706235439e+01 9.81755460563928e+00
87 1.00425414168408e+01 9.84200765912343e+00
88 1.00393046004480e+01 9.86642899323320e+00
89 1.00362677210398e+01 9.89232615597538e+00
90 1.00333326702222e+01 9.92077091295346e+00
91 1.00304190984417e+01 9.95163431119817e+00
92 1.00274924302484e+01 9.98320614724761e+00
93 1.00245832030580e+01 1.00126809229005e+01
94 1.00217818712298e+01 1.00372157022896e+01
95 1.00192174478224e+01 1.00549229065348e+01
96 1.00170334876474e+01 1.00654011519876e+01
97 1.00153609154724e+01 1.00697015600771e+01
98 1.00142801210350e+01 1.00698014812365e+01
99 1.00137749686339e+01 1.00677656407202e+01
100 1.00136989326255e+01 1.00648830006091e+01
100 1.00136989326255e+01 1.00648830006091e+01
101 1.00137674082083e+01 1.00611318434583e+01
102 1.00135836692120e+01 1.00551787890126e+01
103 1.00127001705469e+01 1.00448624179689e+01
104 1.00107128955990e+01 1.00279896008852e+01
105 1.00073732210918e+01 1.00031581615939e+01
106 1.00026863896858e+01 9.97035446256176e+00
107 9.99696129324890e+00 9.93114647843641e+00
108 9.99078911556410e+00 9.88834547941894e+00
109 9.98495363939735e+00 9.84525289783234e+00
110 9.98029333636388e+00 9.80488218664815e+00
111 9.97754787492958e+00 9.76956483721087e+00
112 9.97722552172005e+00 9.74089998776836e+00
113 9.97952448720610e+00 9.71964869280979e+00
114 9.98432949668635e+00 9.70572109422863e+00
115 9.99128565538624e+00 9.69882579496975e+00
116 9.99992834152120e+00 9.69906594532193e+00
117 1.00098244901113e+01 9.70675942684906e+00
118 1.00206778548564e+01 9.72193838510829e+00
119 1.00323618718055e+01 9.74392916146852e+00
120 1.00448741144078e+01 9.77144817149792e+00
121 1.00582353428180e+01 9.80293643028548e+00
122 1.00723772537607e+01 9.83653980628752e+00
123 1.00870562810006e+01 9.86996874359296e+00
124 1.01018143847617e+01 9.90067377124461e+00
125 1.01159953973120e+01 9.92637526075002e+00
126 1.01288196652442e+01 9.94569135970445e+00
127 1.01395052692626e+01 9.95859533688896e+00
128 1.01474034953817e+01 9.96651718147533e+00
129 1.01521107193303e+01 9.97198512417321e+00
130 1.01535310646235e+01 9.97783256102044e+00
131 1.01518709230597e+01 9.98617497185904e+00
132 1.01475657142497e+01 9.99754506682891e+00
133 1.01411666167305e+01 1.00106710657684e+01
134 1.01332318751871e+01 1.00230220357698e+01
135 1.01242581986854e+01 1.00317166064461e+01
136 1.01146544066986e+01 1.00343612487317e+01
137 1.01047332554016e+01 1.00296420246780e+01
138 1.00947014667735e+01 1.00175763327172e+01
139 1.00846531387645e+01 9.99930494674974e+00
140 1.00745857366623e+01 9.97646128131491e+00
141 1.00644400706802e+01 9.95041823440337e+00
142 1.00541501159131e+01 9.92180857541951e+00
143 1.00436834569978e+01 9.89050941872713e+00
144 1.00330649757401e+01 9.85603943350860e+00
145 1.00223855042347e+01 9.81818968302844e+00
146 1.00118066120717e+01 9.77759398920638e+00
147 1.00015635423691e+01 9.73590632972306e+00
148 9.99195808427061e+00 9.69551862637489e+00
149 9.98332973799261e+00 9.65911623085002e+00
150 9.97599905761175e+00 9.62915505877515e+00
151 9.97019367767784e+00 9.60716909686955e+00
152 9.96598267281873e+00 9.59318709200410e+00
153 9.96324605944343e+00 9.58559881047527e+00
154 9.96169276126796e+00 9.58153758556819e+00
155 9.96092625032814e+00 9.57763829311044e+00
156 9.96054315607791e+00 9.57093750799266e+00
157 9.96023482227745e+00 9.55965895377840e+00
158 9.95985352165466e+00 9.54367776307569e+00
159 9.95942460039566e+00 9.52452561463833e+00
160 9.95911205589222e+00 9.50490226824346e+00
161 9.95914975443396e+00 9.48781410600212e+00
162 9.95975278911406e+00 9.47562429341561e+00
163 9.96103890040379e+00 9.46939719079233e+00
164 9.96299147170478e+00 9.46883821286236e+00
165 9.96547099380307e+00 9.47284423942468e+00
166 9.96826097146115e+00 9.48031949605208e+00
167 9.97113131026389e+00 9.49080246783928e+00
168 9.97390346515378e+00 9.50467508257787e+00
169 9.97650055807565e+00 9.52297045210046e+00
170 9.97896696852481e+00 9.54683120799382e+00
171 9.98144993167344e+00 9.57673108800475e+00
172 9.98414386605973e+00 9.61177309775590e+00
173 9.98721435874383e+00 9.64941604907962e+00
174 9.99072987081047e+00 9.68581828149366e+00
175 9.99462784290560e+00 9.71674849920838e+00
176 9.99872910050856e+00 9.73876571566039e+00
177 1.00027910094647e+01 9.75024496509227e+00
178 1.00065753933095e+01 9.75188677631197e+00
179 1.00099096736715e+01 9.74652424002240e+00
180 1.00127256239536e+01 9.73825559652692e+00
181 1.00150707323506e+01 9.73120003142692e+00
182 1.00170870650914e+01 9.72835138795971e+00
183 1.00189588719574e+01 9.73088542644806e+00
184 1.00208370553711e+01 9.73798855694274e+00
185 1.00227676206971e+01 9.74722630488312e+00
186 1.00246552838286e+01 9.75544013816019e+00
187 1.00262844434324e+01 9.75985859738447e+00
188 1.00273887691195e+01 9.75895345517658e+00
189 1.00277400472209e+01 9.75275536148299e+00
190 1.00272200725279e+01 9.74261382746486e+00
191 1.00258549688160e+01 9.73056754269459e+00
192 1.00238089567536e+01 9.71853980670345e+00
193 1.00213474465750e+01 9.70762043885231e+00
194 1.00187805230869e+01 9.69773175124558e+00
195 1.00164016154513e+01 9.68784935173366e+00
196 1.00144402674219e+01 9.67667427007303e+00
197 1.00130444574495e+01 9.66343938720852e+00
198 1.00122912607270e+01 9.64854739476250e+00
199 1.00122066750836e+01 9.63383866331536e+00
200 1.00127732034965e+01 9.62235997490241e+00
68 1.01383594707679e+01 9.59267551611128e+00
69 1.01380701059532e+01 9.56168371312924e+00
70 1.01352290156399e+01 9.54132235576292e+00
71 1.01303782422632e+01 9.53145207033865e+00
72 1.01241807468998e+01 9.53052072472082e+00
73 1.01173118912091e+01 9.53632715678298e+00
74 1.01103471939659e+01 9.54668992740775e+00
75 1.01036629090248e+01 9.55984803752012e+00
76 1.00973931139318e+01 9.57467381743775e+00
77 1.00914805900150e+01 9.59078681449293e+00
78 1.00857806923796e+01 9.60849062320414e+00
79 1.00801732463746e+01 9.62847591791801e+00
80 1.00746211947646e+01 9.65137407697184e+00
81 1.00691682828698e+01 9.67731006830983e+00
82 1.00638992393183e+01 9.70564969348716e+00
83 1.00589006124326e+01 9.73510953408138e+00
84 1.00542402131508e+01 9.76420390471977e+00
85 1.00499602946157e+01 9.79180385249472e+00
86 1.00460706235435e+01 9.81755460564468e+00
87 1.00425414168399e+01 9.84200765912968e+00
88 1.00393046004464e+01 9.86642899324013e+00
89 1.00362677210369e+01 9.89232615598293e+00
90 1.00333326702175e+01 9.92077091296133e+00
91 1.00304190984349e+01 9.95163431120606e+00
92 1.00274924302394e+01 9.98320614725514e+00
93 1.00245832030468e+01 1.00126809229072e+01
94 1.00217818712178e+01 1.00372157022924e+01
95 1.00192174478128e+01 1.00549229065339e+01
96 1.00170334876423e+01 1.00654011519831e+01
97 1.00153609154726e+01 1.00697015600704e+01
98 1.00142801210419e+01 1.00698014812268e+01
99 1.00137749686484e+01 1.00677656407098e+01
100 1.00136989326479e+01 1.00648830006035e+01
100 1.00136989326479e+01 1.00648830006035e+01
101 1.00137674082404e+01 1.00611318434631e+01
102 1.00135836692638e+01 1.00551787890321e+01
103 1.00127001706252e+01 1.00448624180052e+01
104 1.00107128957021e+01 1.00279896009381e+01
105 1.00073732212177e+01 1.00031581616613e+01
106 1.00026863898319e+01 9.97035446264584e+00
107 9.99696129340979e+00 9.93114647853474e+00
108 9.99078911574286e+00 9.88834547952885e+00
109 9.98495363959500e+00 9.84525289795163e+00
110 9.98029333657187e+00 9.80488218677250e+00
111 9.97754787513574e+00 9.76956483733739e+00
112 9.97722552190832e+00 9.74089998789470e+00
113 9.97952448737980e+00 9.71964869293034e+00
114 9.98432949682222e+00 9.70572109433721e+00
115 9.99128565545184e+00 9.69882579506424e+00
116 9.99992834150833e+00 9.69906594541022e+00
117 1.00098244900360e+01 9.70675942693532e+00
118 1.00206778547510e+01 9.72193838520098e+00
119 1.00323618716864e+01 9.74392916157914e+00
120 1.00448741142733e+01 9.77144817163477e+00
121 1.00582353426856e+01 9.80293643045616e+00
122 1.00723772536367e+01 9.83653980649396e+00
123 1.00870562808775e+01 9.86996874383092e+00
124 1.01018143846136e+01 9.90067377150288e+00
125 1.01159953971355e+01 9.92637526102012e+00
126 1.01288196650277e+01 9.94569135999291e+00
127 1.01395052689679e+01 9.95859533719747e+00
128 1.01474034950021e+01 9.96651718180170e+00
129 1.01521107188430e+01 9.97198512451327e+00
130 1.01535310640198e+01 9.97783256135978e+00
131 1.01518709223691e+01 9.98617497219244e+00
132 1.01475657134909e+01 9.99754506714391e+00
133 1.01411666159632e+01 1.00106710660677e+01
134 1.01332318744629e+01 1.00230220360430e+01
135 1.01242581980791e+01 1.00317166066961e+01
136 1.01146544061953e+01 1.00343612489597e+01
137 1.01047332550129e+01 1.00296420248946e+01
138 1.00947014664877e+01 1.00175763329223e+01
139 1.00846531385394e+01 9.99930494695532e+00
140 1.00745857364974e+01 9.97646128152161e+00
141 1.00644400705403e+01 9.95041823460627e+00
142 1.00541501157683e+01 9.92180857562118e+00
143 1.00436834568360e+01 9.89050941892251e+00
144 1.00330649755670e+01 9.85603943369589e+00
145 1.00223855041248e+01 9.81818968320503e+00
146 1.00118066120332e+01 9.77759398937178e+00
147 1.00015635424482e+01 9.73590632987673e+00
148 9.99195808450856e+00 9.69551862651774e+00
149 9.98332973840472e+00 9.65911623099469e+00
150 9.97599905822999e+00 9.62915505892649e+00
151 9.97019367845638e+00 9.60716909703526e+00
152 9.96598267372795e+00 9.59318709218540e+00
153 9.96324606044969e+00 9.58559881066392e+00
154 9.96169276237047e+00 9.58153758575953e+00
155 9.96092625152242e+00 9.57763829328116e+00
156 9.96054315740228e+00 9.57093750810941e+00
157 9.96023482376251e+00 9.55965895382487e+00
158 9.95985352333786e+00 9.54367776304373e+00
159 9.95942460236116e+00 9.52452561453112e+00
160 9.95911205820184e+00 9.50490226807002e+00
161 9.95914975712190e+00 9.48781410580017e+00
162 9.95975279219164e+00 9.47562429324685e+00
163 9.96103890394426e+00 9.46939719071147e+00
164 9.96299147570651e+00 9.46883821294305e+00
165 9.96547099819345e+00 9.47284423972085e+00
166 9.96826097616579e+00 9.48031949660299e+00
167 9.97113131520360e+00 9.49080246868345e+00
168 9.97390347029220e+00 9.50467508368792e+00
169 9.97650056337441e+00 9.52297045344289e+00
170 9.97896697398981e+00 9.54683120949238e+00
171 9.98144993724280e+00 9.57673108957231e+00
172 9.98414387172420e+00 9.61177309931033e+00
173 9.98721436449207e+00 9.64941605055506e+00
174 9.99072987660973e+00 9.68581828287900e+00
175 9.99462784873357e+00 9.71674850053884e+00
176 9.99872910630021e+00 9.73876571701760e+00
177 1.00027910151196e+01 9.75024496660445e+00
178 1.00065753987481e+01 9.75188677811518e+00
179 1.00099096788152e+01 9.74652424221370e+00
180 1.00127256286803e+01 9.73825559920752e+00
181 1.00150707365928e+01 9.73120003464725e+00
182 1.00170870688102e+01 9.72835139174119e+00
183 1.00189588750915e+01 9.73088543078432e+00
184 1.00208370578559e+01 9.73798856175907e+00
185 1.00227676225361e+01 9.74722631009118e+00
186 1.00246552850623e+01 9.75544014363497e+00
187 1.00262844441069e+01 9.75985860295140e+00
188 1.00273887692830e+01 9.75895346064793e+00
189 1.00277400469004e+01 9.75275536661271e+00
190 1.00272200717913e+01 9.74261383198996e+00
191 1.00258549677417e+01 9.73056754639127e+00
192 1.00238089554369e+01 9.71853980943337e+00
193 1.00213474450786e+01 9.70762044056817e+00
194 1.00187805216026e+01 9.69773175201182e+00
195 1.00164016141049e+01 9.68784935170505e+00
196 1.00144402663323e+01 9.67667426952134e+00
197 1.00130444566844e+01 9.66343938641739e+00
198 1.00122912603524e+01 9.64854739402150e+00
199 1.00122066751424e+01 9.63383866285097e+00
200 1.00127732039621e+01 9.62235997484479e+00

6
examples/PACKAGES/colvars/out2.colvars.state
View File

@ -1,17 +1,17 @@
configuration {
step 300
dt 2.000000e+00
version 2020-07-07
version 2024-06-04
}
colvar {
name one
x 9.95315918568411e+00
x 9.9531592295885
}
colvar {
name two
x 9.79318883680258e+00
x 9.7931889789213
}
restraint {

202
examples/PACKAGES/colvars/out2.colvars.traj
View File

@ -1,102 +1,102 @@
# step one two
200 1.00127732034965e+01 9.62235997490241e+00
201 1.00139198864982e+01 9.61766167925624e+00
202 1.00155004339120e+01 9.62284272858813e+00
203 1.00172741972246e+01 9.63964899323068e+00
204 1.00189052021826e+01 9.66786718571673e+00
205 1.00199887119842e+01 9.70521202056400e+00
206 1.00201070660155e+01 9.74782380666112e+00
207 1.00189089093749e+01 9.79114913038349e+00
208 1.00162005540278e+01 9.83091553260188e+00
209 1.00120316562035e+01 9.86409994884863e+00
210 1.00067394529596e+01 9.88955328455197e+00
211 1.00009200584653e+01 9.90798080826055e+00
212 9.99531475905311e+00 9.92127385542524e+00
213 9.99063400342297e+00 9.93157198661852e+00
214 9.98737188807678e+00 9.94051482696048e+00
215 9.98567127567181e+00 9.94885527957784e+00
216 9.98528704043382e+00 9.95646746111755e+00
217 9.98565832937415e+00 9.96275739929720e+00
218 9.98606724184677e+00 9.96730423246689e+00
219 9.98583582550472e+00 9.97036378703713e+00
220 9.98451001643477e+00 9.97292736129215e+00
221 9.98198434901656e+00 9.97627439806637e+00
222 9.97853678731273e+00 9.98127100659218e+00
223 9.97475984191141e+00 9.98785371236258e+00
224 9.97140286510626e+00 9.99492286335624e+00
225 9.96917137580259e+00 1.00005443231922e+01
226 9.96854523900174e+00 1.00023222923235e+01
227 9.96967375964547e+00 9.99790273206806e+00
228 9.97237636771905e+00 9.98555960216881e+00
229 9.97624253505807e+00 9.96473792067690e+00
230 9.98078777310055e+00 9.93636511602182e+00
231 9.98560846780419e+00 9.90275990393703e+00
232 9.99048787217569e+00 9.86710855077386e+00
233 9.99543040822038e+00 9.83269539984149e+00
234 1.00006246021103e+01 9.80221208335553e+00
235 1.00063530848982e+01 9.77738136586701e+00
236 1.00128741709083e+01 9.75887400813685e+00
237 1.00203106975850e+01 9.74632163179798e+00
238 1.00285805371730e+01 9.73844350416337e+00
239 1.00373945897865e+01 9.73349215182819e+00
240 1.00463194539327e+01 9.72980720779576e+00
241 1.00548770491533e+01 9.72611599020063e+00
242 1.00626421174965e+01 9.72152572108181e+00
243 1.00693109823863e+01 9.71531423107737e+00
244 1.00747300690509e+01 9.70668632474813e+00
245 1.00788811512303e+01 9.69472082245661e+00
246 1.00818281591535e+01 9.67872530149764e+00
247 1.00836382918008e+01 9.65899116363609e+00
248 1.00843077585461e+01 9.63702967428387e+00
249 1.00837304601058e+01 9.61431312359133e+00
250 1.00817369874724e+01 9.59193249256670e+00
251 1.00781951382998e+01 9.57162234547176e+00
252 1.00731274409141e+01 9.55557274350384e+00
253 1.00667870632608e+01 9.54560001126946e+00
254 1.00596598859158e+01 9.54253147668434e+00
255 1.00523956909045e+01 9.54593692832520e+00
256 1.00457028282132e+01 9.55423082330650e+00
257 1.00402418669526e+01 9.56514761944992e+00
258 1.00365397691695e+01 9.57641296971103e+00
259 1.00349276270394e+01 9.58620624196598e+00
260 1.00355019919770e+01 9.59332346959128e+00
261 1.00381137097146e+01 9.59732188686984e+00
262 1.00423905760179e+01 9.59837618250971e+00
263 1.00477959188736e+01 9.59679324477687e+00
264 1.00537068007149e+01 9.59269523141530e+00
265 1.00594937260641e+01 9.58610120816249e+00
266 1.00645870781682e+01 9.57722117048002e+00
267 1.00685316571224e+01 9.56668493985151e+00
268 1.00710357823615e+01 9.55556251047062e+00
269 1.00720144042107e+01 9.54520978473172e+00
270 1.00716144493745e+01 9.53703781183182e+00
271 1.00701992199135e+01 9.53227489206590e+00
272 1.00682808706064e+01 9.53173333554826e+00
273 1.00663988075209e+01 9.53554943194497e+00
274 1.00649733063520e+01 9.54299862049767e+00
275 1.00641836485840e+01 9.55262143610080e+00
276 1.00639178664285e+01 9.56271517955029e+00
277 1.00638153921535e+01 9.57192148747872e+00
278 1.00633853985923e+01 9.57957875475062e+00
279 1.00621626720543e+01 9.58572327394556e+00
280 1.00598570838615e+01 9.59085686511578e+00
281 1.00564566071967e+01 9.59567423393283e+00
282 1.00522576614697e+01 9.60085550637412e+00
283 1.00478091897332e+01 9.60690040068280e+00
284 1.00437767664032e+01 9.61396708331890e+00
285 1.00407546813490e+01 9.62178118810825e+00
286 1.00390773261870e+01 9.62975547860500e+00
287 1.00386906040191e+01 9.63733595704590e+00
288 1.00391292740982e+01 9.64435229335154e+00
289 1.00396077171765e+01 9.65114124926381e+00
290 1.00391967746350e+01 9.65843904962787e+00
291 1.00370409303829e+01 9.66713735495098e+00
292 1.00325613495850e+01 9.67798035621834e+00
293 1.00255913568518e+01 9.69130440474672e+00
294 1.00164044158125e+01 9.70689841022156e+00
295 1.00056261321876e+01 9.72399810930261e+00
296 9.99406221883501e+00 9.74140402524052e+00
297 9.98250803362175e+00 9.75776438941627e+00
298 9.97160202027972e+00 9.77203069297329e+00
299 9.96175637151037e+00 9.78379375044905e+00
300 9.95315918568411e+00 9.79318883680258e+00
200 1.00127732039621e+01 9.62235997484479e+00
201 1.00139198873142e+01 9.61766167960114e+00
202 1.00155004349735e+01 9.62284272927993e+00
203 1.00172741984288e+01 9.63964899413135e+00
204 1.00189052034286e+01 9.66786718668113e+00
205 1.00199887131237e+01 9.70521202139326e+00
206 1.00201070669505e+01 9.74782380717117e+00
207 1.00189089099933e+01 9.79114913037297e+00
208 1.00162005542527e+01 9.83091553193592e+00
209 1.00120316559893e+01 9.86409994753053e+00
210 1.00067394522266e+01 9.88955328278264e+00
211 1.00009200570685e+01 9.90798080630807e+00
212 9.99531475670037e+00 9.92127385350745e+00
213 9.99063399978946e+00 9.93157198491364e+00
214 9.98737188290188e+00 9.94051482558046e+00
215 9.98567126870035e+00 9.94885527853167e+00
216 9.98528703143402e+00 9.95646746044078e+00
217 9.98565831825084e+00 9.96275739920543e+00
218 9.98606722850532e+00 9.96730423316541e+00
219 9.98583581006681e+00 9.97036378874527e+00
220 9.98450999905139e+00 9.97292736402649e+00
221 9.98198432974296e+00 9.97627440161597e+00
222 9.97853676608100e+00 9.98127101043889e+00
223 9.97475981847134e+00 9.98785371579891e+00
224 9.97140283904510e+00 9.99492286559338e+00
225 9.96917134637541e+00 1.00005443234936e+01
226 9.96854520536988e+00 1.00023222900809e+01
227 9.96967372102824e+00 9.99790272698630e+00
228 9.97237632329275e+00 9.98555959429830e+00
229 9.97624248419111e+00 9.96473791046628e+00
230 9.98078771543058e+00 9.93636510426670e+00
231 9.98560840329183e+00 9.90275989164257e+00
232 9.99048780094848e+00 9.86710853890991e+00
233 9.99543033063032e+00 9.83269538913306e+00
234 1.00006245185513e+01 9.80221207423406e+00
235 1.00063529959328e+01 9.77738135842695e+00
236 1.00128740773079e+01 9.75887400220566e+00
237 1.00203106003782e+01 9.74632162713091e+00
238 1.00285804376080e+01 9.73844350045589e+00
239 1.00373944894039e+01 9.73349214878674e+00
240 1.00463193546284e+01 9.72980720512224e+00
241 1.00548769529672e+01 9.72611598750665e+00
242 1.00626420263492e+01 9.72152571786963e+00
243 1.00693108979996e+01 9.71531422666390e+00
244 1.00747299927796e+01 9.70668631833486e+00
245 1.00788810840328e+01 9.69472081315003e+00
246 1.00818281015229e+01 9.67872528846535e+00
247 1.00836382438846e+01 9.65899114629446e+00
248 1.00843077202414e+01 9.63702965268533e+00
249 1.00837304312378e+01 9.61431309843794e+00
250 1.00817369677632e+01 9.59193246490958e+00
251 1.00781951275561e+01 9.57162231665577e+00
252 1.00731274389447e+01 9.55557271498134e+00
253 1.00667870699195e+01 9.54559998431332e+00
254 1.00596599010604e+01 9.54253145213164e+00
255 1.00523957143832e+01 9.54593690642836e+00
256 1.00457028598538e+01 9.55423080384305e+00
257 1.00402419064054e+01 9.56514760196478e+00
258 1.00365398159221e+01 9.57641295373454e+00
259 1.00349276804438e+01 9.58620622717253e+00
260 1.00355020510841e+01 9.59332345585722e+00
261 1.00381137733017e+01 9.59732187421620e+00
262 1.00423906427137e+01 9.59837617102817e+00
263 1.00477959872900e+01 9.59679323453788e+00
264 1.00537068694862e+01 9.59269522224878e+00
265 1.00594937939774e+01 9.58610119961332e+00
266 1.00645871442695e+01 9.57722116190429e+00
267 1.00685317208695e+01 9.56668493059359e+00
268 1.00710358435525e+01 9.55556250017823e+00
269 1.00720144628669e+01 9.54520977349603e+00
270 1.00716145056864e+01 9.53703780013997e+00
271 1.00701992741473e+01 9.53227488069496e+00
272 1.00682809229059e+01 9.53173332532930e+00
273 1.00663988579612e+01 9.53554942356440e+00
274 1.00649733547668e+01 9.54299861430164e+00
275 1.00641836945973e+01 9.55262143202964e+00
276 1.00639179095174e+01 9.56271517715327e+00
277 1.00638154316074e+01 9.57192148613520e+00
278 1.00633854335686e+01 9.57957875400668e+00
279 1.00621627016565e+01 9.58572327370357e+00
280 1.00598571070638e+01 9.59085686592320e+00
281 1.00564566229803e+01 9.59567423699651e+00
282 1.00522576689401e+01 9.60085551333600e+00
283 1.00478091881844e+01 9.60690041329352e+00
284 1.00437767554115e+01 9.61396710318380e+00
285 1.00407546608873e+01 9.62178121653831e+00
286 1.00390772967935e+01 9.62975551670189e+00
287 1.00386905666453e+01 9.63733600598964e+00
288 1.00391292301728e+01 9.64435235461356e+00
289 1.00396076684883e+01 9.65114132457984e+00
290 1.00391967232973e+01 9.65843914091158e+00
291 1.00370408787737e+01 9.66713746391752e+00
292 1.00325613002434e+01 9.67798048381559e+00
293 1.00255913122523e+01 9.69130455064462e+00
294 1.00164043783898e+01 9.70689857240811e+00
295 1.00056261042358e+01 9.72399828398139e+00
296 9.99406220236070e+00 9.74140420689973e+00
297 9.98250803047048e+00 9.75776457125789e+00
298 9.97160203186903e+00 9.77203086770013e+00
299 9.96175639897897e+00 9.78379391142304e+00
300 9.95315922958854e+00 9.79318897892133e+00

4
examples/PACKAGES/colvars/peptide2.colvars.state
View File

@ -1,12 +1,12 @@
configuration {
step 100
dt 2.000000e+00
version 2020-07-07
version 2024-06-04
}
colvar {
name one
x 1.00387423506482e+01
x 10.038742350674
}
restraint {

76
examples/PACKAGES/colvars/peptide2.colvars.traj
View File

@ -20,16 +20,16 @@
18 9.41602481112176e+00
19 9.44413580740584e+00
20 9.49001346044027e+00
21 9.55036359015270e+00
22 9.62258602486444e+00
23 9.70460545744668e+00
21 9.55036359015271e+00
22 9.62258602486445e+00
23 9.70460545744666e+00
24 9.79475465622561e+00
25 9.89135302429916e+00
26 9.99213332770717e+00
25 9.89135302429913e+00
26 9.99213332770716e+00
27 1.00938522423366e+01
28 1.01925371414626e+01
29 1.02845129002944e+01
30 1.03676671987640e+01
30 1.03676671987639e+01
31 1.04416385355998e+01
32 1.05071349561950e+01
33 1.05650463398331e+01
@ -41,39 +41,39 @@
39 1.07331870068021e+01
40 1.07158913924701e+01
41 1.06789115566470e+01
42 1.06198840652253e+01
42 1.06198840652254e+01
43 1.05380097743725e+01
44 1.04346581978275e+01
45 1.03132910149185e+01
46 1.01792819503691e+01
46 1.01792819503692e+01
47 1.00398949454818e+01
48 9.90373650268307e+00
49 9.77934647164350e+00
50 9.67343955381284e+00
51 9.58957255517495e+00
52 9.52771577288560e+00
53 9.48463495848957e+00
54 9.45495747488851e+00
55 9.43277083061229e+00
56 9.41329510571902e+00
57 9.39417852043035e+00
49 9.77934647164349e+00
50 9.67343955381283e+00
51 9.58957255517494e+00
52 9.52771577288559e+00
53 9.48463495848955e+00
54 9.45495747488850e+00
55 9.43277083061230e+00
56 9.41329510571900e+00
57 9.39417852043034e+00
58 9.37607916767444e+00
59 9.36243879601093e+00
60 9.35853234890725e+00
61 9.36993739187210e+00
62 9.40084256925489e+00
59 9.36243879601092e+00
60 9.35853234890724e+00
61 9.36993739187209e+00
62 9.40084256925487e+00
63 9.45286356660258e+00
64 9.52464585631223e+00
65 9.61230948096192e+00
66 9.71074418990813e+00
67 9.81507236552599e+00
68 9.92117974657176e+00
69 1.00244259961919e+01
66 9.71074418990814e+00
67 9.81507236552600e+00
68 9.92117974657179e+00
69 1.00244259961920e+01
70 1.01178306268727e+01
71 1.01986985644537e+01
71 1.01986985644538e+01
72 1.02671003889995e+01
73 1.03213098011429e+01
74 1.03597236984298e+01
73 1.03213098011430e+01
74 1.03597236984299e+01
75 1.03817789163109e+01
76 1.03880650963390e+01
77 1.03809140245635e+01
@ -82,21 +82,21 @@
80 1.03243676495902e+01
81 1.03082131278348e+01
82 1.02961310659179e+01
83 1.02862115513553e+01
83 1.02862115513552e+01
84 1.02756073299153e+01
85 1.02618115461408e+01
86 1.02435127550163e+01
87 1.02212112849545e+01
88 1.01972788307491e+01
89 1.01743918261207e+01
89 1.01743918261206e+01
90 1.01538328424605e+01
91 1.01363005552771e+01
92 1.01223066231827e+01
93 1.01118037967830e+01
92 1.01223066231826e+01
93 1.01118037967829e+01
94 1.01038502876980e+01
95 1.00967012947728e+01
96 1.00885779123137e+01
97 1.00784256309007e+01
98 1.00661429612272e+01
99 1.00524913461711e+01
100 1.00387423506482e+01
95 1.00967012947726e+01
96 1.00885779123133e+01
97 1.00784256308996e+01
98 1.00661429612359e+01
99 1.00524913461887e+01
100 1.00387423506735e+01