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LAMMPS (17 Jan 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# Created by charmm2lammps v1.9.1 on Sun Jan 28 05:50:21 EST 2018
# Command: charmm2lammps.pl -border=2.0 -cmap=36 -ions -water all36_prot 1gb1
units real
neigh_modify delay 2 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8 12
pair_modify mix arithmetic
kspace_style pppm 1e-6
# Modify following line to point to the desired CMAP file
fix cmap all cmap charmm36.cmap
Reading potential file charmm36.cmap with DATE: 2016-09-26
fix_modify cmap energy yes
read_data 1gb1.data fix cmap crossterm CMAP
orthogonal box = (-20.8413 -14.5892 -13.805) to (23.4963 14.9692 10.827)
2 by 2 by 1 MPI processor grid
reading atoms ...
2833 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
24 = max dihedrals/atom
scanning impropers ...
2 = max impropers/atom
reading bonds ...
2177 bonds
reading angles ...
2209 angles
reading dihedrals ...
2707 dihedrals
reading impropers ...
137 impropers
4 = max # of 1-2 neighbors
9 = max # of 1-3 neighbors
17 = max # of 1-4 neighbors
21 = max # of special neighbors
special_bonds charmm
thermo 10
thermo_style multi
timestep 1.0
minimize 0.0 0.0 50 200
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.278254
grid = 45 32 30
stencil order = 5
estimated absolute RMS force accuracy = 0.000317429
estimated relative force accuracy = 9.55928e-07
using double precision FFTs
3d grid and FFT values/proc = 25530 11520
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 5 4
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
Per MPI rank memory allocation (min/avg/max) = 24.54 | 24.61 | 24.65 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -3304.5599 KinEng = 0.0000 Temp = 0.0000
PotEng = -3304.5599 E_bond = 169.6834 E_angle = 103.6483
E_dihed = 583.9669 E_impro = 0.0335 E_vdwl = -776.3982
E_coul = 35482.9694 E_long = -38851.5191 Press = 3844.7433
---------------- Step 10 ----- CPU = 0.3473 (sec) ----------------
TotEng = -4930.6259 KinEng = 0.0000 Temp = 0.0000
PotEng = -4930.6259 E_bond = 104.7992 E_angle = 181.4386
E_dihed = 584.0895 E_impro = 7.5537 E_vdwl = -1028.4574
E_coul = 34837.9592 E_long = -39590.5863 Press = -8420.5689
---------------- Step 20 ----- CPU = 0.7554 (sec) ----------------
TotEng = -5457.1158 KinEng = 0.0000 Temp = 0.0000
PotEng = -5457.1158 E_bond = 121.1716 E_angle = 243.0784
E_dihed = 580.3183 E_impro = 8.9483 E_vdwl = -1040.3321
E_coul = 34593.3894 E_long = -39923.3583 Press = -9942.5587
---------------- Step 30 ----- CPU = 1.1694 (sec) ----------------
TotEng = -6057.2086 KinEng = 0.0000 Temp = 0.0000
PotEng = -6057.2086 E_bond = 120.1005 E_angle = 267.0579
E_dihed = 570.6124 E_impro = 9.3921 E_vdwl = -1025.6144
E_coul = 34318.6209 E_long = -40277.2340 Press = -11617.6026
---------------- Step 40 ----- CPU = 1.6505 (sec) ----------------
TotEng = -6520.0628 KinEng = 0.0000 Temp = 0.0000
PotEng = -6520.0628 E_bond = 135.8622 E_angle = 293.3665
E_dihed = 558.0537 E_impro = 8.6211 E_vdwl = -968.6884
E_coul = 33877.9402 E_long = -40381.7851 Press = -12652.4710
---------------- Step 50 ----- CPU = 2.1052 (sec) ----------------
TotEng = -6931.3243 KinEng = 0.0000 Temp = 0.0000
PotEng = -6931.3243 E_bond = 147.5166 E_angle = 290.5234
E_dihed = 550.9597 E_impro = 9.4741 E_vdwl = -794.7620
E_coul = 33347.2827 E_long = -40437.2965 Press = -11322.9412
Loop time of 2.10544 on 4 procs for 50 steps with 2833 atoms
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-3304.55988409 -6893.73171135 -6931.32434601
Force two-norm initial, final = 1135.31 300.792
Force max component initial, final = 107.634 93.2558
Final line search alpha, max atom move = 0.00152738 0.142437
Iterations, force evaluations = 50 82
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.5485 | 1.5674 | 1.5856 | 1.4 | 74.44
Bond | 0.017887 | 0.020853 | 0.024278 | 1.6 | 0.99
Kspace | 0.41442 | 0.43099 | 0.45053 | 2.5 | 20.47
Neigh | 0.052102 | 0.052125 | 0.052147 | 0.0 | 2.48
Comm | 0.023884 | 0.024002 | 0.024059 | 0.0 | 1.14
Output | 0.00030303 | 0.00051945 | 0.0011663 | 0.0 | 0.02
Modify | 0.0015671 | 0.0018674 | 0.0021205 | 0.5 | 0.09
Other | | 0.007689 | | | 0.37
Nlocal: 708.25 ave 728 max 693 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 9301.25 ave 9410 max 9200 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 356382 ave 367163 max 347323 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 1425526
Ave neighs/atom = 503.186
Ave special neighs/atom = 4.67702
Neighbor list builds = 3
Dangerous builds = 0
reset_timestep 0
fix 1 all nve
fix 2 all shake 1e-6 500 0 m 1.0 a 112
168 = # of size 2 clusters
64 = # of size 3 clusters
41 = # of size 4 clusters
658 = # of frozen angles
velocity all create 0.0 12345678 dist uniform
restart 500 1gb1.restart1 1gb1.restart2
dump 1 all atom 100 1gb1.dump
dump_modify 1 image yes scale yes
thermo 100
run 1000
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.278254
grid = 45 32 30
stencil order = 5
estimated absolute RMS force accuracy = 0.000317429
estimated relative force accuracy = 9.55928e-07
using double precision FFTs
3d grid and FFT values/proc = 25530 11520
Per MPI rank memory allocation (min/avg/max) = 25.34 | 25.4 | 25.44 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -7157.1195 KinEng = 0.0000 Temp = 0.0000
PotEng = -7157.1195 E_bond = 59.0052 E_angle = 144.8137
E_dihed = 550.9597 E_impro = 9.4741 E_vdwl = -794.7620
E_coul = 33347.2827 E_long = -40437.2965 Press = -11653.0907
---------------- Step 100 ----- CPU = 2.0713 (sec) ----------------
TotEng = -6731.9859 KinEng = 736.6132 Temp = 121.4739
PotEng = -7468.5991 E_bond = 51.6809 E_angle = 141.9715
E_dihed = 539.0053 E_impro = 6.5800 E_vdwl = -138.7778
E_coul = 32438.3099 E_long = -40470.2744 Press = -6545.1453
---------------- Step 200 ----- CPU = 4.1194 (sec) ----------------
TotEng = -6732.1577 KinEng = 1137.9916 Temp = 187.6647
PotEng = -7870.1494 E_bond = 54.1322 E_angle = 155.0534
E_dihed = 530.3471 E_impro = 6.0821 E_vdwl = 581.9109
E_coul = 31309.7031 E_long = -40477.5339 Press = -1108.1567
---------------- Step 300 ----- CPU = 6.2051 (sec) ----------------
TotEng = -6732.2356 KinEng = 1205.1394 Temp = 198.7380
PotEng = -7937.3749 E_bond = 50.7295 E_angle = 154.0262
E_dihed = 541.0277 E_impro = 9.6153 E_vdwl = 553.9794
E_coul = 31264.5100 E_long = -40483.0651 Press = -1179.2736
---------------- Step 400 ----- CPU = 8.3309 (sec) ----------------
TotEng = -6732.3498 KinEng = 1263.7920 Temp = 208.4103
PotEng = -7996.1418 E_bond = 59.5441 E_angle = 159.8690
E_dihed = 531.3170 E_impro = 9.8105 E_vdwl = 572.2021
E_coul = 31187.5411 E_long = -40486.5450 Press = -1312.0304
---------------- Step 500 ----- CPU = 10.5236 (sec) ----------------
TotEng = -6732.2697 KinEng = 1225.7309 Temp = 202.1337
PotEng = -7958.0006 E_bond = 52.7184 E_angle = 169.2353
E_dihed = 529.7384 E_impro = 10.4859 E_vdwl = 489.7017
E_coul = 31300.5731 E_long = -40480.8862 Press = -1431.7699
---------------- Step 600 ----- CPU = 12.7351 (sec) ----------------
TotEng = -6732.2989 KinEng = 1238.7683 Temp = 204.2837
PotEng = -7971.0672 E_bond = 56.2994 E_angle = 173.1005
E_dihed = 530.0426 E_impro = 10.5372 E_vdwl = 535.7865
E_coul = 31234.7342 E_long = -40486.0690 Press = -1402.7109
---------------- Step 700 ----- CPU = 14.9715 (sec) ----------------
TotEng = -6732.3516 KinEng = 1309.3540 Temp = 215.9239
PotEng = -8041.7056 E_bond = 59.3741 E_angle = 177.8374
E_dihed = 526.2153 E_impro = 12.2105 E_vdwl = 536.7845
E_coul = 31152.4306 E_long = -40484.9510 Press = -1448.7774
---------------- Step 800 ----- CPU = 17.2110 (sec) ----------------
TotEng = -6732.3114 KinEng = 1299.2723 Temp = 214.2613
PotEng = -8031.5837 E_bond = 55.8605 E_angle = 178.5243
E_dihed = 534.2468 E_impro = 11.5427 E_vdwl = 560.2428
E_coul = 31143.0967 E_long = -40486.6330 Press = -737.0231
---------------- Step 900 ----- CPU = 19.4334 (sec) ----------------
TotEng = -6732.4712 KinEng = 1299.4505 Temp = 214.2907
PotEng = -8031.9217 E_bond = 61.2314 E_angle = 181.8029
E_dihed = 536.4906 E_impro = 12.4741 E_vdwl = 475.8515
E_coul = 31223.2733 E_long = -40494.0221 Press = -1853.8183
---------------- Step 1000 ----- CPU = 21.6519 (sec) ----------------
TotEng = -6732.4953 KinEng = 1325.4723 Temp = 218.5819
PotEng = -8057.9676 E_bond = 55.0903 E_angle = 187.1899
E_dihed = 524.1709 E_impro = 13.3778 E_vdwl = 510.4710
E_coul = 31176.6501 E_long = -40497.1637 Press = -1649.1418
Loop time of 21.6521 on 4 procs for 1000 steps with 2833 atoms
Performance: 3.990 ns/day, 6.014 hours/ns, 46.185 timesteps/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 13.758 | 14.312 | 14.767 | 11.1 | 66.10
Bond | 0.14719 | 0.17763 | 0.21239 | 5.5 | 0.82
Kspace | 5.0774 | 5.5813 | 6.2275 | 18.7 | 25.78
Neigh | 0.81074 | 0.8116 | 0.81234 | 0.1 | 3.75
Comm | 0.28366 | 0.34314 | 0.41466 | 10.2 | 1.58
Output | 0.018707 | 0.019262 | 0.020673 | 0.6 | 0.09
Modify | 0.33949 | 0.35308 | 0.36488 | 1.7 | 1.63
Other | | 0.05392 | | | 0.25
Nlocal: 708.25 ave 747 max 669 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 9164.5 ave 9383 max 8916 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 357504 ave 379770 max 327897 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 1430018
Ave neighs/atom = 504.772
Ave special neighs/atom = 4.67702
Neighbor list builds = 40
Dangerous builds = 0
Total wall time: 0:00:23
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