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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13471 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2015-05-15 19:36:25 +00:00
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LAMMPS (30 Apr 2015)
# 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
thermo_style multi
thermo 50
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
fix 2 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
group peptide type <= 12
84 atoms in group peptide
#dump 1 peptide atom 10 dump.peptide
#dump 2 peptide image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
#dump_modify 2 pad 3
#dump 3 peptide movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
#dump_modify 3 pad 3
#compute bnd all property/local btype batom1 batom2
#dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]
run 300
PPPM initialization ...
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 ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
master list distance cutoff = 12
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
Memory usage per processor = 15.1545 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005
PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726
E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
E_coul = 26772.2646 E_long = -33907.9271 Press = -845.4774
---------------- Step 50 ----- CPU = 0.9953 (sec) ----------------
TotEng = -5247.5490 KinEng = 1132.4011 Temp = 281.4748
PotEng = -6379.9501 E_bond = 12.2118 E_angle = 31.7365
E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1771
E_coul = 26804.4490 E_long = -33907.7002 Press = -1331.7980
SHAKE stats (type/ave/delta) on step 100
4 1.111 7.80799e-07
6 0.997 1.06209e-06
8 1.08 6.20485e-07
10 1.111 6.23445e-07
12 1.08 2.68063e-07
14 0.96 0
18 0.957201 5.38018e-06
31 104.52 0.000502316
---------------- Step 100 ----- CPU = 1.9893 (sec) ----------------
TotEng = -5257.9972 KinEng = 1078.0556 Temp = 267.9664
PotEng = -6336.0528 E_bond = 14.4828 E_angle = 43.4429
E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3266
E_coul = 26786.6841 E_long = -33906.5620 Press = -648.6637
---------------- Step 150 ----- CPU = 3.0374 (sec) ----------------
TotEng = -5287.2845 KinEng = 1098.6036 Temp = 273.0739
PotEng = -6385.8881 E_bond = 17.4924 E_angle = 32.8593
E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9686
E_coul = 26717.2583 E_long = -33907.2812 Press = -333.1888
SHAKE stats (type/ave/delta) on step 200
4 1.111 2.18836e-07
6 0.997 1.50855e-07
8 1.08 6.58342e-08
10 1.111 5.5535e-07
12 1.08 1.99243e-07
14 0.96 0
18 0.957201 3.59666e-06
31 104.52 0.000388186
---------------- Step 200 ----- CPU = 4.0247 (sec) ----------------
TotEng = -5308.4527 KinEng = 1100.5055 Temp = 273.5467
PotEng = -6408.9582 E_bond = 18.2714 E_angle = 33.3035
E_dihed = 16.8150 E_impro = 2.6053 E_vdwl = 686.3264
E_coul = 26736.1130 E_long = -33902.3928 Press = -1470.3831
---------------- Step 250 ----- CPU = 5.0700 (sec) ----------------
TotEng = -5294.1807 KinEng = 1071.1619 Temp = 266.2529
PotEng = -6365.3426 E_bond = 14.2022 E_angle = 39.1953
E_dihed = 19.4555 E_impro = 3.1387 E_vdwl = 753.5416
E_coul = 26713.8467 E_long = -33908.7226 Press = -188.8007
SHAKE stats (type/ave/delta) on step 300
4 1.111 3.78262e-06
6 0.997001 3.50131e-06
8 1.08 2.0932e-06
10 1.111 5.64324e-06
12 1.08 2.10399e-06
14 0.96 0
18 0.957202 7.67973e-06
31 104.52 0.000806336
---------------- Step 300 ----- CPU = 6.1288 (sec) ----------------
TotEng = -5251.4333 KinEng = 1123.6266 Temp = 279.2937
PotEng = -6375.0599 E_bond = 14.2249 E_angle = 38.4712
E_dihed = 18.1324 E_impro = 2.3700 E_vdwl = 715.4550
E_coul = 26745.4115 E_long = -33909.1249 Press = -469.5254
Loop time of 6.12878 on 1 procs for 300 steps with 2004 atoms
Pair time (%) = 4.85547 (79.2241)
Bond time (%) = 0.0136414 (0.222579)
Kspce time (%) = 0.488526 (7.97101)
Neigh time (%) = 0.675145 (11.016)
Comm time (%) = 0.0268722 (0.438458)
Outpt time (%) = 0.000172138 (0.00280869)
Other time (%) = 0.0689545 (1.12509)
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11181 ave 11181 max 11181 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 708029 ave 708029 max 708029 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708029
Ave neighs/atom = 353.308
Ave special neighs/atom = 2.34032
Neighbor list builds = 26
Dangerous builds = 0

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LAMMPS (30 Apr 2015)
# 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
thermo_style multi
thermo 50
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
fix 2 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
group peptide type <= 12
84 atoms in group peptide
#dump 1 peptide atom 10 dump.peptide
#dump 2 peptide image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
#dump_modify 2 pad 3
#dump 3 peptide movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
#dump_modify 3 pad 3
#compute bnd all property/local btype batom1 batom2
#dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]
run 300
PPPM initialization ...
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 ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
master list distance cutoff = 12
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
Memory usage per processor = 14.4096 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005
PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726
E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
E_coul = 26772.2646 E_long = -33907.9271 Press = -845.4774
---------------- Step 50 ----- CPU = 0.2787 (sec) ----------------
TotEng = -5247.5490 KinEng = 1132.4011 Temp = 281.4748
PotEng = -6379.9501 E_bond = 12.2118 E_angle = 31.7365
E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1771
E_coul = 26804.4490 E_long = -33907.7002 Press = -1331.7981
SHAKE stats (type/ave/delta) on step 100
4 1.111 7.80799e-07
6 0.997 1.06209e-06
8 1.08 6.20484e-07
10 1.111 6.23445e-07
12 1.08 2.68063e-07
14 0.96 0
18 0.957201 5.38018e-06
31 104.52 0.000502316
---------------- Step 100 ----- CPU = 0.5603 (sec) ----------------
TotEng = -5257.9973 KinEng = 1078.0556 Temp = 267.9664
PotEng = -6336.0529 E_bond = 14.4828 E_angle = 43.4429
E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3266
E_coul = 26786.6840 E_long = -33906.5620 Press = -648.6639
---------------- Step 150 ----- CPU = 0.8498 (sec) ----------------
TotEng = -5287.2844 KinEng = 1098.6036 Temp = 273.0739
PotEng = -6385.8881 E_bond = 17.4924 E_angle = 32.8593
E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9685
E_coul = 26717.2583 E_long = -33907.2812 Press = -333.1895
SHAKE stats (type/ave/delta) on step 200
4 1.111 2.18836e-07
6 0.997 1.50856e-07
8 1.08 6.58343e-08
10 1.111 5.55349e-07
12 1.08 1.99243e-07
14 0.96 0
18 0.957201 3.59666e-06
31 104.52 0.000388184
---------------- Step 200 ----- CPU = 1.1308 (sec) ----------------
TotEng = -5308.4528 KinEng = 1100.5056 Temp = 273.5467
PotEng = -6408.9584 E_bond = 18.2714 E_angle = 33.3035
E_dihed = 16.8150 E_impro = 2.6053 E_vdwl = 686.3261
E_coul = 26736.1131 E_long = -33902.3928 Press = -1470.3871
---------------- Step 250 ----- CPU = 1.4236 (sec) ----------------
TotEng = -5294.1809 KinEng = 1071.1623 Temp = 266.2530
PotEng = -6365.3432 E_bond = 14.2022 E_angle = 39.1953
E_dihed = 19.4555 E_impro = 3.1387 E_vdwl = 753.5412
E_coul = 26713.8465 E_long = -33908.7226 Press = -188.8077
SHAKE stats (type/ave/delta) on step 300
4 1.111 3.78266e-06
6 0.997001 3.50137e-06
8 1.08 2.09322e-06
10 1.111 5.64331e-06
12 1.08 2.10401e-06
14 0.96 0
18 0.957202 7.67991e-06
31 104.52 0.000806336
---------------- Step 300 ----- CPU = 1.7191 (sec) ----------------
TotEng = -5251.4350 KinEng = 1123.6256 Temp = 279.2935
PotEng = -6375.0606 E_bond = 14.2249 E_angle = 38.4712
E_dihed = 18.1324 E_impro = 2.3700 E_vdwl = 715.4557
E_coul = 26745.4100 E_long = -33909.1249 Press = -469.5450
Loop time of 1.71912 on 4 procs for 300 steps with 2004 atoms
Pair time (%) = 1.23855 (72.0454)
Bond time (%) = 0.0039109 (0.227494)
Kspce time (%) = 0.17904 (10.4146)
Neigh time (%) = 0.169081 (9.83531)
Comm time (%) = 0.0679622 (3.95331)
Outpt time (%) = 0.000325799 (0.0189515)
Other time (%) = 0.0602537 (3.50491)
Nlocal: 501 ave 508 max 490 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Nghost: 6586.25 ave 6628 max 6548 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 177007 ave 180562 max 170212 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Total # of neighbors = 708028
Ave neighs/atom = 353.307
Ave special neighs/atom = 2.34032
Neighbor list builds = 26
Dangerous builds = 0