164 lines
7.8 KiB
Groff
164 lines
7.8 KiB
Groff
LAMMPS (23 Jun 2022)
|
|
# solvated ubiquitin molecule with AMOEBA force field
|
|
|
|
units real
|
|
boundary p p p
|
|
atom_modify sort 0 0.0
|
|
|
|
atom_style amoeba
|
|
|
|
bond_style class2
|
|
angle_style amoeba
|
|
dihedral_style fourier
|
|
improper_style amoeba
|
|
|
|
# per-atom properties required by AMOEBA or HIPPO
|
|
|
|
fix amtype all property/atom i_amtype ghost yes
|
|
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
|
|
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
|
|
|
|
fix pit all amoeba/pitorsion
|
|
fix_modify pit energy yes
|
|
fix bit all amoeba/bitorsion bitorsion.ubiquitin.data
|
|
fix_modify bit energy yes
|
|
|
|
# read data file
|
|
|
|
read_data data.ubiquitin fix amtype NULL "Tinker Types" fix pit "pitorsion types" "PiTorsion Coeffs" fix pit pitorsions PiTorsions fix bit bitorsions BiTorsions
|
|
Reading data file ...
|
|
orthogonal box = (0 0 0) to (54.99 41.91 41.91)
|
|
2 by 1 by 2 MPI processor grid
|
|
reading atoms ...
|
|
9737 atoms
|
|
scanning bonds ...
|
|
4 = max bonds/atom
|
|
scanning angles ...
|
|
6 = max angles/atom
|
|
scanning dihedrals ...
|
|
18 = max dihedrals/atom
|
|
scanning impropers ...
|
|
3 = max impropers/atom
|
|
reading bonds ...
|
|
6908 bonds
|
|
reading angles ...
|
|
5094 angles
|
|
reading dihedrals ...
|
|
3297 dihedrals
|
|
reading impropers ...
|
|
651 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
|
|
9 = max # of 1-3 neighbors
|
|
19 = max # of 1-4 neighbors
|
|
21 = max # of special neighbors
|
|
special bonds CPU = 0.001 seconds
|
|
read_data CPU = 0.072 seconds
|
|
|
|
pair_style amoeba
|
|
pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
|
|
Reading potential file amoeba_ubiquitin.prm with DATE: 2022-07-05
|
|
Skipping section: AMOEBA Protein Force Field Atom Classes
|
|
Skipping section: Torsion-Torsion Parameters
|
|
Skipping section: Biopolymer Atom Type Conversions
|
|
Reading potential file amoeba_ubiquitin.key with DATE: 2022-07-05
|
|
|
|
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
|
|
Finding 1-2 1-3 1-4 neighbors ...
|
|
special bond factors lj: 0.5 0.5 0.5
|
|
special bond factors coul: 0.5 0.5 0.5
|
|
4 = max # of 1-2 neighbors
|
|
9 = max # of 1-3 neighbors
|
|
19 = max # of 1-4 neighbors
|
|
58 = max # of 1-5 neighbors
|
|
21 = max # of special neighbors
|
|
special bonds CPU = 0.002 seconds
|
|
|
|
# thermo output
|
|
|
|
compute virial all pressure NULL virial
|
|
|
|
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
|
|
|
|
#dump 1 all custom 10 dump.ubiquitin id type x y z fx fy fz
|
|
#dump_modify 1 sort id
|
|
|
|
# dynamics
|
|
|
|
fix 1 all nve
|
|
|
|
thermo 1
|
|
run 10
|
|
AMOEBA force field settings
|
|
hal: cut 12 taper 10.8 vscale 0 0 1 1
|
|
multipole: cut 7 aewald 0.4 bsorder 5 FFT 60 48 48 mscale 0 0 0.4 1
|
|
polar: cut 7 aewald 0.5 bsorder 5 FFT 60 48 48
|
|
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
|
|
precondition: cut 4.5
|
|
Generated 0 of 15 mixed pair_coeff terms from geometric mixing rule
|
|
Neighbor list info ...
|
|
update every 1 steps, delay 10 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 14
|
|
ghost atom cutoff = 14
|
|
binsize = 7, bins = 8 6 6
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair amoeba, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/newton
|
|
stencil: half/bin/3d
|
|
bin: standard
|
|
AMOEBA group count: 3196
|
|
Per MPI rank memory allocation (min/avg/max) = 144.2 | 144.7 | 145.4 Mbytes
|
|
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
|
|
0 0 -35338.057 2856.5938 1955.5431 224.37609 65.00809 5101.5211 -30247.585 -6336.5196 -5795.4272 -6329.8149 -6884.3167 349.52657 77.164877 652.41925
|
|
1 29.61379 -35356.153 2037.3541 1840.7883 223.90217 64.293945 4166.3385 -30341.522 -6486.773 -6452.8463 -6841.5982 -7386.1106 311.38025 120.72605 545.35513
|
|
2 78.518242 -35383.65 825.39919 1538.3909 222.55095 62.191009 2648.5321 -30467.814 -5502.9841 -6410.2998 -6396.1829 -6937.8137 217.3515 210.76948 294.28051
|
|
3 88.8921 -35402.11 938.99299 1162.2914 220.5271 58.832521 2380.644 -30453.516 -1929.5417 -3331.1291 -2769.7218 -3350.5733 117.32302 279.72705 31.237776
|
|
4 68.740402 -35477.589 2048.0659 858.03795 218.14277 54.460022 3178.7066 -30316.325 2041.1138 594.25938 1665.7799 1030.8539 66.230421 304.28296 -155.80224
|
|
5 76.267862 -35707.869 2206.6534 736.37385 215.75693 49.401674 3208.1859 -30299.377 2276.9276 536.21124 1893.4621 1258.492 92.097191 299.65604 -228.58369
|
|
6 118.24373 -36092.77 1166.179 815.59206 213.67399 44.022297 2239.4673 -30435.629 -1677.8051 -3988.2428 -2669.6848 -3247.7207 197.42472 285.87129 -162.35459
|
|
7 137.7204 -36521.444 782.87113 1026.745 212.04289 38.686259 2060.3452 -30479.082 -5987.83 -8386.8104 -7363.188 -7888.261 357.00835 253.66346 32.827786
|
|
8 112.66452 -36897.181 1750.0569 1269.152 210.83571 33.742799 3263.7874 -30379.432 -7886.4081 -9703.2601 -9043.015 -9555.2908 490.76046 182.31259 278.727
|
|
9 88.237359 -37209.906 2695.1766 1454.55 209.91331 29.503458 4389.1434 -30276.565 -8202.16 -9492.368 -9110.7037 -9639.2288 502.55699 107.82333 443.6705
|
|
10 108.86756 -37474.988 2240.4603 1523.7936 209.10313 26.208515 3999.5656 -30333.279 -8468.4347 -9956.923 -9709.5874 -10224.682 365.98214 95.262991 425.12746
|
|
Loop time of 6.03244 on 4 procs for 10 steps with 9737 atoms
|
|
|
|
Performance: 0.143 ns/day, 167.568 hours/ns, 1.658 timesteps/s
|
|
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
|
|
|
AMOEBA timing breakdown:
|
|
Init time: 0.0192504 0.32%
|
|
Hal time: 1.86975 31.05%
|
|
Mpole time: 0.633256 10.52%
|
|
Induce time: 2.26029 37.54%
|
|
Polar time: 1.23884 20.57%
|
|
Total time: 6.02139
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 6.0202 | 6.0215 | 6.0228 | 0.0 | 99.82
|
|
Bond | 0.0029895 | 0.0033805 | 0.0036579 | 0.4 | 0.06
|
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
Comm | 0.0044978 | 0.0059188 | 0.0070446 | 1.5 | 0.10
|
|
Output | 0.00055049 | 0.00062352 | 0.00079826 | 0.0 | 0.01
|
|
Modify | 0.00067451 | 0.00071394 | 0.00074612 | 0.0 | 0.01
|
|
Other | | 0.0003294 | | | 0.01
|
|
|
|
Nlocal: 2434.25 ave 2498 max 2390 min
|
|
Histogram: 1 1 0 0 1 0 0 0 0 1
|
|
Nghost: 16683.2 ave 16765 max 16568 min
|
|
Histogram: 1 0 0 1 0 0 0 0 0 2
|
|
Neighs: 1.40982e+06 ave 1.52088e+06 max 1.30717e+06 min
|
|
Histogram: 2 0 0 0 0 0 0 0 1 1
|
|
|
|
Total # of neighbors = 5639296
|
|
Ave neighs/atom = 579.16155
|
|
Ave special neighs/atom = 3.1364897
|
|
Neighbor list builds = 0
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:07
|