LAMMPS (24 Mar 2022) 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 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 = 0.001 seconds read_data CPU = 0.011 seconds neighbor 2.0 bin neigh_modify delay 5 timestep 2.0 thermo_style multi thermo 50 group tmd id 1:6 6 atoms in group tmd fix 1 all nvt temp 275.0 275.0 100.0 tchain 1 fix 0 tmd tmd 0.1 tmd.target 100 tmd.log Reading TMD target file tmd.target ... 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 find clusters CPU = 0.000 seconds 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 ... using 12-bit tables for long-range coulomb (src/kspace.cpp:340) 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 9 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) = 19.78 | 19.78 | 19.78 Mbytes ------------ Step 0 ----- CPU = 0 (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 = -837.0112 ------------ Step 50 ----- CPU = 0.6301453 (sec) ------------- TotEng = -5001.6799 KinEng = 1319.3760 Temp = 327.9501 PotEng = -6321.0559 E_bond = 17.4415 E_angle = 42.4509 E_dihed = 25.0839 E_impro = 4.4025 E_vdwl = 725.7619 E_coul = 26771.0015 E_long = -33907.1980 Press = -1.1409 SHAKE stats (type/ave/delta/count) on step 100 Bond: 4 1.11096 0.000146572 9 Bond: 6 0.996997 7.55911e-06 6 Bond: 8 1.08 8.22449e-06 9 Bond: 10 1.11099 3.00424e-05 8 Bond: 12 1.08 6.53505e-06 9 Bond: 14 0.95999 0 1 Bond: 18 0.957195 4.74892e-05 1280 Angle: 31 104.52 0.00446577 640 ------------ Step 100 ----- CPU = 1.251267 (sec) ------------- TotEng = -5114.3221 KinEng = 1168.2996 Temp = 290.3979 PotEng = -6282.6217 E_bond = 45.5470 E_angle = 87.5725 E_dihed = 26.1332 E_impro = 1.8662 E_vdwl = 791.5291 E_coul = 26670.6791 E_long = -33905.9488 Press = -29.3446 ------------ Step 150 ----- CPU = 1.869158 (sec) ------------- TotEng = -5302.3058 KinEng = 1211.4300 Temp = 301.1186 PotEng = -6513.7358 E_bond = 51.4069 E_angle = 82.5752 E_dihed = 31.1298 E_impro = 4.3390 E_vdwl = 764.0550 E_coul = 26461.8974 E_long = -33909.1392 Press = -1204.2714 SHAKE stats (type/ave/delta/count) on step 200 Bond: 4 1.11094 0.000292869 9 Bond: 6 0.996989 3.13206e-05 6 Bond: 8 1.07999 4.4723e-05 9 Bond: 10 1.111 1.08895e-05 8 Bond: 12 1.07999 1.42694e-05 9 Bond: 14 0.959976 0 1 Bond: 18 0.957195 8.58256e-05 1280 Angle: 31 104.52 0.00597861 640 ------------ Step 200 ----- CPU = 2.48933 (sec) ------------- TotEng = -5785.4658 KinEng = 1048.7220 Temp = 260.6751 PotEng = -6834.1879 E_bond = 21.7304 E_angle = 48.3249 E_dihed = 20.5973 E_impro = 2.0603 E_vdwl = 818.9175 E_coul = 26165.9672 E_long = -33911.7854 Press = -1228.5741 ------------ Step 250 ----- CPU = 3.119859 (sec) ------------- TotEng = -6108.4578 KinEng = 828.5247 Temp = 205.9419 PotEng = -6936.9825 E_bond = 26.5971 E_angle = 68.2771 E_dihed = 36.1232 E_impro = 5.2092 E_vdwl = 884.1147 E_coul = 25955.7300 E_long = -33913.0338 Press = -1365.4744 SHAKE stats (type/ave/delta/count) on step 300 Bond: 4 1.11174 0.0109853 9 Bond: 6 0.996999 1.94772e-06 6 Bond: 8 1.08 3.97091e-06 9 Bond: 10 1.111 2.52635e-06 8 Bond: 12 1.08 1.24444e-06 9 Bond: 14 0.96 0 1 Bond: 18 0.9572 1.22873e-05 1280 Angle: 31 104.52 0.00134864 640 ------------ Step 300 ----- CPU = 3.74524 (sec) ------------- TotEng = -5492.5012 KinEng = 1315.6902 Temp = 327.0339 PotEng = -6808.1914 E_bond = 88.7967 E_angle = 104.4231 E_dihed = 28.2383 E_impro = 43.5062 E_vdwl = 992.5311 E_coul = 25849.1502 E_long = -33914.8370 Press = 268.8004 Loop time of 3.74527 on 1 procs for 300 steps with 2004 atoms Performance: 13.841 ns/day, 1.734 hours/ns, 80.101 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 | 2.9399 | 2.9399 | 2.9399 | 0.0 | 78.50 Bond | 0.0069522 | 0.0069522 | 0.0069522 | 0.0 | 0.19 Kspace | 0.25203 | 0.25203 | 0.25203 | 0.0 | 6.73 Neigh | 0.48624 | 0.48624 | 0.48624 | 0.0 | 12.98 Comm | 0.016948 | 0.016948 | 0.016948 | 0.0 | 0.45 Output | 0.00023689 | 0.00023689 | 0.00023689 | 0.0 | 0.01 Modify | 0.039476 | 0.039476 | 0.039476 | 0.0 | 1.05 Other | | 0.003502 | | | 0.09 Nlocal: 2004 ave 2004 max 2004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11242 ave 11242 max 11242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 710782 ave 710782 max 710782 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 710782 Ave neighs/atom = 354.68164 Ave special neighs/atom = 2.3403194 Neighbor list builds = 32 Dangerous builds = 1 Total wall time: 0:00:03