257 lines
12 KiB
Plaintext
257 lines
12 KiB
Plaintext
LAMMPS (5 Oct 2016)
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package omp 0
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WARNING: OpenMP support not enabled during compilation; using 1 thread only. (../fix_omp.cpp:123)
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# Created by charmm2lammps v1.9.1 on Wed Oct 5 18:08:55 EDT 2016
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# Command: charmm2lammps.pl -water -ions -border=2.0 all36_prot 1gb1
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units real
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neigh_modify delay 2 every 1
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atom_style full
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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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pair_style lj/charmm/coul/long 8 12
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pair_modify mix arithmetic
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kspace_style pppm 1e-6
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read_data 1gb1.data
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orthogonal box = (-20.8413 -14.5892 -13.805) to (23.4963 14.9692 10.827)
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2 by 2 by 2 MPI processor grid
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reading atoms ...
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2833 atoms
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scanning bonds ...
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4 = 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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24 = max dihedrals/atom
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scanning impropers ...
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2 = max impropers/atom
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reading bonds ...
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2177 bonds
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reading angles ...
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2209 angles
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reading dihedrals ...
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2707 dihedrals
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reading impropers ...
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137 impropers
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4 = max # of 1-2 neighbors
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9 = max # of 1-3 neighbors
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17 = max # of 1-4 neighbors
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21 = max # of special neighbors
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special_bonds charmm
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thermo 10
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thermo_style multi
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timestep 1.0
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minimize 0.0 0.0 50 200
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WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
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PPPM initialization ...
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WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
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G vector (1/distance) = 0.278254
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grid = 45 32 30
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stencil order = 5
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estimated absolute RMS force accuracy = 0.000317429
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estimated relative force accuracy = 9.55928e-07
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using double precision FFTs
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3d grid and FFT values/proc = 15180 5760
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Last active /omp style is kspace_style pppm/omp
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Neighbor list info ...
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1 neighbor list requests
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 14
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ghost atom cutoff = 14
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binsize = 7 -> bins = 7 5 4
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Memory usage per processor = 19.7492 Mbytes
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---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
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TotEng = -3599.1065 KinEng = 0.0000 Temp = 0.0000
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PotEng = -3599.1065 E_bond = 169.6834 E_angle = 103.6483
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E_dihed = 583.9669 E_impro = 0.0335 E_vdwl = -776.0899
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E_coul = 35419.6941 E_long = -39100.0428 Press = 3623.5803
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---------------- Step 10 ----- CPU = 0.2563 (sec) ----------------
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TotEng = -5168.1778 KinEng = 0.0000 Temp = 0.0000
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PotEng = -5168.1778 E_bond = 120.7538 E_angle = 171.5023
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E_dihed = 583.0143 E_impro = 6.5958 E_vdwl = -1034.8022
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E_coul = 34737.4006 E_long = -39752.6424 Press = -10232.1944
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---------------- Step 20 ----- CPU = 0.4597 (sec) ----------------
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TotEng = -5784.4945 KinEng = 0.0000 Temp = 0.0000
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PotEng = -5784.4945 E_bond = 110.1359 E_angle = 262.6659
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E_dihed = 573.8164 E_impro = 8.5071 E_vdwl = -1050.9646
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E_coul = 34464.2659 E_long = -40152.9212 Press = -10843.0328
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---------------- Step 30 ----- CPU = 0.6813 (sec) ----------------
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TotEng = -6342.0862 KinEng = 0.0000 Temp = 0.0000
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PotEng = -6342.0862 E_bond = 146.0247 E_angle = 272.7224
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E_dihed = 557.6616 E_impro = 7.1074 E_vdwl = -984.4028
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E_coul = 34031.1722 E_long = -40372.3718 Press = -13674.9873
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---------------- Step 40 ----- CPU = 0.8599 (sec) ----------------
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TotEng = -6821.3956 KinEng = 0.0000 Temp = 0.0000
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PotEng = -6821.3956 E_bond = 147.4491 E_angle = 271.5247
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E_dihed = 548.2429 E_impro = 7.1832 E_vdwl = -873.4714
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E_coul = 33514.8072 E_long = -40437.1312 Press = -12024.8390
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---------------- Step 50 ----- CPU = 1.0662 (sec) ----------------
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TotEng = -7278.3435 KinEng = 0.0000 Temp = 0.0000
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PotEng = -7278.3435 E_bond = 181.9934 E_angle = 288.9107
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E_dihed = 541.0050 E_impro = 7.1673 E_vdwl = -501.3825
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E_coul = 32665.6923 E_long = -40461.7297 Press = -10391.9829
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Loop time of 1.06631 on 8 procs for 50 steps with 2833 atoms
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99.3% CPU use with 8 MPI tasks x 1 OpenMP threads
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Minimization stats:
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Stopping criterion = max iterations
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Energy initial, next-to-last, final =
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-3599.10649881 -7238.80368107 -7278.34352699
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Force two-norm initial, final = 1109.81 247.325
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Force max component initial, final = 107.492 37.5055
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Final line search alpha, max atom move = 0.00133024 0.0498915
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Iterations, force evaluations = 50 87
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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 | 0.46313 | 0.53526 | 0.61611 | 6.9 | 50.20
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Bond | 0.0070326 | 0.01008 | 0.013407 | 1.8 | 0.95
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Kspace | 0.3364 | 0.41785 | 0.49165 | 8.0 | 39.19
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Neigh | 0.035014 | 0.035175 | 0.035337 | 0.1 | 3.30
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Comm | 0.058533 | 0.05973 | 0.060792 | 0.3 | 5.60
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Output | 0.00039005 | 0.00040504 | 0.00049496 | 0.2 | 0.04
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Modify | 0.0015707 | 0.0022006 | 0.0025775 | 0.6 | 0.21
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Other | | 0.005615 | | | 0.53
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Nlocal: 354.125 ave 376 max 344 min
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Histogram: 3 1 0 1 2 0 0 0 0 1
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Nghost: 7405 ave 7531 max 7307 min
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Histogram: 1 2 1 0 0 1 1 1 0 1
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Neighs: 178281 ave 194848 max 158123 min
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Histogram: 2 0 1 0 0 1 0 1 2 1
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Total # of neighbors = 1426250
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Ave neighs/atom = 503.442
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Ave special neighs/atom = 4.67702
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Neighbor list builds = 4
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Dangerous builds = 0
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reset_timestep 0
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fix 1 all nve
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fix 2 all shake 1e-6 500 0 m 1.0 a 112
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168 = # of size 2 clusters
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64 = # of size 3 clusters
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41 = # of size 4 clusters
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658 = # of frozen angles
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velocity all create 0.0 12345678 dist uniform
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restart 500 1gb1.restart1 1gb1.restart2
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dump 1 all atom 100 1gb1.dump
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dump_modify 1 image yes scale yes
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thermo 100
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run 1000
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PPPM initialization ...
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WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
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G vector (1/distance) = 0.278254
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grid = 45 32 30
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stencil order = 5
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estimated absolute RMS force accuracy = 0.000317429
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estimated relative force accuracy = 9.55928e-07
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using double precision FFTs
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3d grid and FFT values/proc = 15180 5760
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Last active /omp style is kspace_style pppm/omp
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Neighbor list info ...
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1 neighbor list requests
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update every 1 steps, delay 2 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 14
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ghost atom cutoff = 14
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binsize = 7 -> bins = 7 5 4
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Memory usage per processor = 20.5221 Mbytes
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---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
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TotEng = -7547.0017 KinEng = 0.0000 Temp = 0.0000
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PotEng = -7547.0017 E_bond = 52.4535 E_angle = 149.7924
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E_dihed = 541.0050 E_impro = 7.1673 E_vdwl = -501.3825
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E_coul = 32665.6923 E_long = -40461.7297 Press = -9600.9476
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---------------- Step 100 ----- CPU = 0.8242 (sec) ----------------
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TotEng = -7049.9503 KinEng = 688.1123 Temp = 113.4757
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PotEng = -7738.0625 E_bond = 53.8035 E_angle = 139.7846
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E_dihed = 529.5460 E_impro = 6.1806 E_vdwl = 52.8666
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E_coul = 31951.7370 E_long = -40471.9810 Press = -5991.4443
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---------------- Step 200 ----- CPU = 1.6765 (sec) ----------------
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TotEng = -7050.0350 KinEng = 956.0848 Temp = 157.6667
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PotEng = -8006.1198 E_bond = 47.1331 E_angle = 140.9769
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E_dihed = 517.5474 E_impro = 5.7244 E_vdwl = 635.2166
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E_coul = 31127.8100 E_long = -40480.5282 Press = -920.9624
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---------------- Step 300 ----- CPU = 2.5246 (sec) ----------------
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TotEng = -7050.0984 KinEng = 1049.7346 Temp = 173.1104
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PotEng = -8099.8330 E_bond = 47.4551 E_angle = 156.5090
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E_dihed = 520.6006 E_impro = 9.4008 E_vdwl = 451.0904
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E_coul = 31202.3817 E_long = -40487.2707 Press = -2352.9550
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---------------- Step 400 ----- CPU = 3.3982 (sec) ----------------
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TotEng = -7050.1671 KinEng = 1099.2465 Temp = 181.2753
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PotEng = -8149.4136 E_bond = 56.6375 E_angle = 164.5897
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E_dihed = 528.8356 E_impro = 8.8390 E_vdwl = 525.0114
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E_coul = 31060.0380 E_long = -40493.3650 Press = -2146.9087
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---------------- Step 500 ----- CPU = 4.2800 (sec) ----------------
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TotEng = -7050.2027 KinEng = 1134.4924 Temp = 187.0877
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PotEng = -8184.6951 E_bond = 53.5903 E_angle = 169.1090
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E_dihed = 522.9488 E_impro = 7.9830 E_vdwl = 496.8404
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E_coul = 31058.9967 E_long = -40494.1633 Press = -2537.1829
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---------------- Step 600 ----- CPU = 5.1548 (sec) ----------------
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TotEng = -7050.1894 KinEng = 1122.6756 Temp = 185.1390
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PotEng = -8172.8649 E_bond = 47.9283 E_angle = 168.7967
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E_dihed = 518.7200 E_impro = 9.2011 E_vdwl = 499.6778
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E_coul = 31076.1916 E_long = -40493.3805 Press = -1939.2216
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---------------- Step 700 ----- CPU = 6.0377 (sec) ----------------
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TotEng = -7050.2850 KinEng = 1154.4452 Temp = 190.3781
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PotEng = -8204.7301 E_bond = 54.3594 E_angle = 183.8772
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E_dihed = 513.0797 E_impro = 9.6842 E_vdwl = 522.0052
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E_coul = 31008.3632 E_long = -40496.0990 Press = -2059.4885
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---------------- Step 800 ----- CPU = 6.9161 (sec) ----------------
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TotEng = -7050.2852 KinEng = 1146.2741 Temp = 189.0306
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PotEng = -8196.5593 E_bond = 48.8126 E_angle = 171.3411
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E_dihed = 525.8682 E_impro = 10.5588 E_vdwl = 538.6905
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E_coul = 31003.8447 E_long = -40495.6752 Press = -1458.5181
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---------------- Step 900 ----- CPU = 7.8101 (sec) ----------------
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TotEng = -7050.3025 KinEng = 1154.2134 Temp = 190.3398
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PotEng = -8204.5159 E_bond = 51.1010 E_angle = 177.9642
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E_dihed = 520.6908 E_impro = 8.9539 E_vdwl = 521.5994
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E_coul = 31012.6307 E_long = -40497.4560 Press = -1683.9131
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---------------- Step 1000 ----- CPU = 8.7313 (sec) ----------------
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TotEng = -7050.3166 KinEng = 1179.9351 Temp = 194.5816
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PotEng = -8230.2517 E_bond = 57.8905 E_angle = 190.1556
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E_dihed = 518.1288 E_impro = 10.0403 E_vdwl = 557.6413
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E_coul = 30933.6472 E_long = -40497.7554 Press = -1643.1247
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Loop time of 8.73139 on 8 procs for 1000 steps with 2833 atoms
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Performance: 9.895 ns/day, 2.425 hours/ns, 114.529 timesteps/s
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99.6% CPU use with 8 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 | 3.2841 | 3.856 | 4.393 | 17.3 | 44.16
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Bond | 0.041216 | 0.074389 | 0.11041 | 7.2 | 0.85
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Kspace | 2.8668 | 3.4354 | 4.0036 | 18.9 | 39.35
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Neigh | 0.3024 | 0.30315 | 0.30402 | 0.1 | 3.47
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Comm | 0.58794 | 0.60511 | 0.61362 | 1.0 | 6.93
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Output | 0.010607 | 0.010696 | 0.010783 | 0.0 | 0.12
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Modify | 0.40802 | 0.41482 | 0.42598 | 0.8 | 4.75
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Other | | 0.03184 | | | 0.36
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Nlocal: 354.125 ave 390 max 323 min
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Histogram: 2 0 2 0 1 0 0 0 1 2
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Nghost: 7219.12 ave 7453 max 6941 min
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Histogram: 1 1 1 1 0 0 0 0 2 2
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Neighs: 179095 ave 217661 max 144647 min
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Histogram: 1 0 1 1 1 2 1 0 0 1
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Total # of neighbors = 1432758
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Ave neighs/atom = 505.739
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Ave special neighs/atom = 4.67702
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Neighbor list builds = 39
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Dangerous builds = 0
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Total wall time: 0:00:09
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