211 lines
8.7 KiB
Groff
211 lines
8.7 KiB
Groff
LAMMPS (24 Mar 2022)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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# Solvated 5-mer peptide
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units real
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atom_style full
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pair_style lj/charmm/coul/long 8.0 10.0 10.0
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bond_style harmonic
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angle_style charmm
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dihedral_style charmm
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improper_style harmonic
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kspace_style pppm 0.0001
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read_data data.peptide
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Reading data file ...
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orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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2004 atoms
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reading velocities ...
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2004 velocities
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scanning bonds ...
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3 = max bonds/atom
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scanning angles ...
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6 = max angles/atom
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scanning dihedrals ...
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14 = max dihedrals/atom
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scanning impropers ...
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1 = max impropers/atom
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reading bonds ...
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1365 bonds
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reading angles ...
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786 angles
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reading dihedrals ...
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207 dihedrals
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reading impropers ...
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12 impropers
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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4 = max # of 1-2 neighbors
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7 = max # of 1-3 neighbors
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14 = max # of 1-4 neighbors
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18 = max # of special neighbors
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special bonds CPU = 0.001 seconds
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read_data CPU = 0.011 seconds
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neighbor 2.0 bin
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neigh_modify delay 5
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timestep 2.0
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thermo_style multi
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thermo 50
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group tmd id 1:6
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6 atoms in group tmd
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fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
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fix 0 tmd tmd 0.1 tmd.target 100 tmd.log
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Reading TMD target file tmd.target ...
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fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
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19 = # of size 2 clusters
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6 = # of size 3 clusters
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3 = # of size 4 clusters
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640 = # of frozen angles
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find clusters CPU = 0.000 seconds
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group peptide type <= 12
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84 atoms in group peptide
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#dump 1 peptide atom 10 dump.peptide
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#dump 2 peptide image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
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#dump_modify 2 pad 3
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#dump 3 peptide movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
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#dump_modify 3 pad 3
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#compute bnd all property/local btype batom1 batom2
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#dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]
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run 300
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:340)
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G vector (1/distance) = 0.26872465
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grid = 15 15 15
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stencil order = 5
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estimated absolute RMS force accuracy = 0.022820853
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estimated relative force accuracy = 6.872432e-05
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using double precision FFTW3
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3d grid and FFT values/proc = 10648 3375
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generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
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Neighbor list info ...
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update every 1 steps, delay 5 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 12
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ghost atom cutoff = 12
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binsize = 6, bins = 5 5 5
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/charmm/coul/long, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d
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bin: standard
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SHAKE stats (type/ave/delta/count) on step 0
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Bond: 4 1.111 1.44264e-05 9
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Bond: 6 0.996998 7.26967e-06 6
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Bond: 8 1.08 1.32536e-05 9
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Bond: 10 1.111 1.22749e-05 8
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Bond: 12 1.08 1.11767e-05 9
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Bond: 14 0.96 0 1
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Bond: 18 0.957206 4.37979e-05 1280
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Angle: 31 104.519 0.00396029 640
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Per MPI rank memory allocation (min/avg/max) = 19.78 | 19.78 | 19.78 Mbytes
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------------ Step 0 ----- CPU = 0 (sec) -------------
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TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005
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PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726
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E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
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E_coul = 26772.2646 E_long = -33907.9271 Press = -837.0112
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------------ Step 50 ----- CPU = 0.6301453 (sec) -------------
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TotEng = -5001.6799 KinEng = 1319.3760 Temp = 327.9501
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PotEng = -6321.0559 E_bond = 17.4415 E_angle = 42.4509
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E_dihed = 25.0839 E_impro = 4.4025 E_vdwl = 725.7619
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E_coul = 26771.0015 E_long = -33907.1980 Press = -1.1409
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SHAKE stats (type/ave/delta/count) on step 100
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Bond: 4 1.11096 0.000146572 9
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Bond: 6 0.996997 7.55911e-06 6
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Bond: 8 1.08 8.22449e-06 9
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Bond: 10 1.11099 3.00424e-05 8
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Bond: 12 1.08 6.53505e-06 9
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Bond: 14 0.95999 0 1
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Bond: 18 0.957195 4.74892e-05 1280
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Angle: 31 104.52 0.00446577 640
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------------ Step 100 ----- CPU = 1.251267 (sec) -------------
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TotEng = -5114.3221 KinEng = 1168.2996 Temp = 290.3979
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PotEng = -6282.6217 E_bond = 45.5470 E_angle = 87.5725
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E_dihed = 26.1332 E_impro = 1.8662 E_vdwl = 791.5291
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E_coul = 26670.6791 E_long = -33905.9488 Press = -29.3446
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------------ Step 150 ----- CPU = 1.869158 (sec) -------------
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TotEng = -5302.3058 KinEng = 1211.4300 Temp = 301.1186
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PotEng = -6513.7358 E_bond = 51.4069 E_angle = 82.5752
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E_dihed = 31.1298 E_impro = 4.3390 E_vdwl = 764.0550
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E_coul = 26461.8974 E_long = -33909.1392 Press = -1204.2714
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SHAKE stats (type/ave/delta/count) on step 200
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Bond: 4 1.11094 0.000292869 9
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Bond: 6 0.996989 3.13206e-05 6
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Bond: 8 1.07999 4.4723e-05 9
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Bond: 10 1.111 1.08895e-05 8
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Bond: 12 1.07999 1.42694e-05 9
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Bond: 14 0.959976 0 1
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Bond: 18 0.957195 8.58256e-05 1280
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Angle: 31 104.52 0.00597861 640
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------------ Step 200 ----- CPU = 2.48933 (sec) -------------
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TotEng = -5785.4658 KinEng = 1048.7220 Temp = 260.6751
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PotEng = -6834.1879 E_bond = 21.7304 E_angle = 48.3249
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E_dihed = 20.5973 E_impro = 2.0603 E_vdwl = 818.9175
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E_coul = 26165.9672 E_long = -33911.7854 Press = -1228.5741
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------------ Step 250 ----- CPU = 3.119859 (sec) -------------
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TotEng = -6108.4578 KinEng = 828.5247 Temp = 205.9419
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PotEng = -6936.9825 E_bond = 26.5971 E_angle = 68.2771
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E_dihed = 36.1232 E_impro = 5.2092 E_vdwl = 884.1147
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E_coul = 25955.7300 E_long = -33913.0338 Press = -1365.4744
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SHAKE stats (type/ave/delta/count) on step 300
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Bond: 4 1.11174 0.0109853 9
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Bond: 6 0.996999 1.94772e-06 6
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Bond: 8 1.08 3.97091e-06 9
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Bond: 10 1.111 2.52635e-06 8
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Bond: 12 1.08 1.24444e-06 9
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Bond: 14 0.96 0 1
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Bond: 18 0.9572 1.22873e-05 1280
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Angle: 31 104.52 0.00134864 640
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------------ Step 300 ----- CPU = 3.74524 (sec) -------------
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TotEng = -5492.5012 KinEng = 1315.6902 Temp = 327.0339
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PotEng = -6808.1914 E_bond = 88.7967 E_angle = 104.4231
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E_dihed = 28.2383 E_impro = 43.5062 E_vdwl = 992.5311
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E_coul = 25849.1502 E_long = -33914.8370 Press = 268.8004
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Loop time of 3.74527 on 1 procs for 300 steps with 2004 atoms
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Performance: 13.841 ns/day, 1.734 hours/ns, 80.101 timesteps/s
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99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 2.9399 | 2.9399 | 2.9399 | 0.0 | 78.50
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Bond | 0.0069522 | 0.0069522 | 0.0069522 | 0.0 | 0.19
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Kspace | 0.25203 | 0.25203 | 0.25203 | 0.0 | 6.73
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Neigh | 0.48624 | 0.48624 | 0.48624 | 0.0 | 12.98
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Comm | 0.016948 | 0.016948 | 0.016948 | 0.0 | 0.45
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Output | 0.00023689 | 0.00023689 | 0.00023689 | 0.0 | 0.01
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Modify | 0.039476 | 0.039476 | 0.039476 | 0.0 | 1.05
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Other | | 0.003502 | | | 0.09
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Nlocal: 2004 ave 2004 max 2004 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 11242 ave 11242 max 11242 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 710782 ave 710782 max 710782 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 710782
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Ave neighs/atom = 354.68164
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Ave special neighs/atom = 2.3403194
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Neighbor list builds = 32
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Dangerous builds = 1
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Total wall time: 0:00:03
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