added 1GB1 example from Robert Latour and update 1AC7 example files (326fdf2c) · Commits · 郑智淋 / lammps

tools/ch2lmp/example-cmap/1gb1.data

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tools/ch2lmp/example-cmap/1gb1.in

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		# Created by charmm2lammps v1.9.1 on Wed Oct 5 18:08:55 EDT 2016
		# Command: charmm2lammps.pl -water -ions -border=2.0 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

		read_data 1gb1.data

		special_bonds charmm
		thermo 10
		thermo_style multi
		timestep 1.0

		minimize 0.0 0.0 50 200

		reset_timestep 0
		fix 1 all nve
		fix 2 all shake 1e-6 500 0 m 1.0 a 112
		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

tools/ch2lmp/example-cmap/1gb1.log

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		LAMMPS (5 Oct 2016)
		package omp 0
		WARNING: OpenMP support not enabled during compilation; using 1 thread only. (../fix_omp.cpp:123)
		# Created by charmm2lammps v1.9.1 on Wed Oct 5 18:08:55 EDT 2016
		# Command: charmm2lammps.pl -water -ions -border=2.0 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

		read_data 1gb1.data
		orthogonal box = (-20.8413 -14.5892 -13.805) to (23.4963 14.9692 10.827)
		2 by 2 by 2 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: Resetting reneighboring criteria during minimization (../min.cpp:168)
		PPPM initialization ...
		WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
		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 = 15180 5760
		Last active /omp style is kspace_style pppm/omp
		Neighbor list info ...
		1 neighbor list requests
		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
		Memory usage per processor = 19.7492 Mbytes
		---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
		TotEng = -3599.1065 KinEng = 0.0000 Temp = 0.0000
		PotEng = -3599.1065 E_bond = 169.6834 E_angle = 103.6483
		E_dihed = 583.9669 E_impro = 0.0335 E_vdwl = -776.0899
		E_coul = 35419.6941 E_long = -39100.0428 Press = 3623.5803
		---------------- Step 10 ----- CPU = 0.2563 (sec) ----------------
		TotEng = -5168.1778 KinEng = 0.0000 Temp = 0.0000
		PotEng = -5168.1778 E_bond = 120.7538 E_angle = 171.5023
		E_dihed = 583.0143 E_impro = 6.5958 E_vdwl = -1034.8022
		E_coul = 34737.4006 E_long = -39752.6424 Press = -10232.1944
		---------------- Step 20 ----- CPU = 0.4597 (sec) ----------------
		TotEng = -5784.4945 KinEng = 0.0000 Temp = 0.0000
		PotEng = -5784.4945 E_bond = 110.1359 E_angle = 262.6659
		E_dihed = 573.8164 E_impro = 8.5071 E_vdwl = -1050.9646
		E_coul = 34464.2659 E_long = -40152.9212 Press = -10843.0328
		---------------- Step 30 ----- CPU = 0.6813 (sec) ----------------
		TotEng = -6342.0862 KinEng = 0.0000 Temp = 0.0000
		PotEng = -6342.0862 E_bond = 146.0247 E_angle = 272.7224
		E_dihed = 557.6616 E_impro = 7.1074 E_vdwl = -984.4028
		E_coul = 34031.1722 E_long = -40372.3718 Press = -13674.9873
		---------------- Step 40 ----- CPU = 0.8599 (sec) ----------------
		TotEng = -6821.3956 KinEng = 0.0000 Temp = 0.0000
		PotEng = -6821.3956 E_bond = 147.4491 E_angle = 271.5247
		E_dihed = 548.2429 E_impro = 7.1832 E_vdwl = -873.4714
		E_coul = 33514.8072 E_long = -40437.1312 Press = -12024.8390
		---------------- Step 50 ----- CPU = 1.0662 (sec) ----------------
		TotEng = -7278.3435 KinEng = 0.0000 Temp = 0.0000
		PotEng = -7278.3435 E_bond = 181.9934 E_angle = 288.9107
		E_dihed = 541.0050 E_impro = 7.1673 E_vdwl = -501.3825
		E_coul = 32665.6923 E_long = -40461.7297 Press = -10391.9829
		Loop time of 1.06631 on 8 procs for 50 steps with 2833 atoms

		99.3% CPU use with 8 MPI tasks x 1 OpenMP threads

		Minimization stats:
		Stopping criterion = max iterations
		Energy initial, next-to-last, final =
		-3599.10649881 -7238.80368107 -7278.34352699
		Force two-norm initial, final = 1109.81 247.325
		Force max component initial, final = 107.492 37.5055
		Final line search alpha, max atom move = 0.00133024 0.0498915
		Iterations, force evaluations = 50 87

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 0.46313 \| 0.53526 \| 0.61611 \| 6.9 \| 50.20
		Bond \| 0.0070326 \| 0.01008 \| 0.013407 \| 1.8 \| 0.95
		Kspace \| 0.3364 \| 0.41785 \| 0.49165 \| 8.0 \| 39.19
		Neigh \| 0.035014 \| 0.035175 \| 0.035337 \| 0.1 \| 3.30
		Comm \| 0.058533 \| 0.05973 \| 0.060792 \| 0.3 \| 5.60
		Output \| 0.00039005 \| 0.00040504 \| 0.00049496 \| 0.2 \| 0.04
		Modify \| 0.0015707 \| 0.0022006 \| 0.0025775 \| 0.6 \| 0.21
		Other \| \| 0.005615 \| \| \| 0.53

		Nlocal: 354.125 ave 376 max 344 min
		Histogram: 3 1 0 1 2 0 0 0 0 1
		Nghost: 7405 ave 7531 max 7307 min
		Histogram: 1 2 1 0 0 1 1 1 0 1
		Neighs: 178281 ave 194848 max 158123 min
		Histogram: 2 0 1 0 0 1 0 1 2 1

		Total # of neighbors = 1426250
		Ave neighs/atom = 503.442
		Ave special neighs/atom = 4.67702
		Neighbor list builds = 4
		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:316)
		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 = 15180 5760
		Last active /omp style is kspace_style pppm/omp
		Neighbor list info ...
		1 neighbor list requests
		update every 1 steps, delay 2 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
		Memory usage per processor = 20.5221 Mbytes
		---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
		TotEng = -7547.0017 KinEng = 0.0000 Temp = 0.0000
		PotEng = -7547.0017 E_bond = 52.4535 E_angle = 149.7924
		E_dihed = 541.0050 E_impro = 7.1673 E_vdwl = -501.3825
		E_coul = 32665.6923 E_long = -40461.7297 Press = -9600.9476
		---------------- Step 100 ----- CPU = 0.8242 (sec) ----------------
		TotEng = -7049.9503 KinEng = 688.1123 Temp = 113.4757
		PotEng = -7738.0625 E_bond = 53.8035 E_angle = 139.7846
		E_dihed = 529.5460 E_impro = 6.1806 E_vdwl = 52.8666
		E_coul = 31951.7370 E_long = -40471.9810 Press = -5991.4443
		---------------- Step 200 ----- CPU = 1.6765 (sec) ----------------
		TotEng = -7050.0350 KinEng = 956.0848 Temp = 157.6667
		PotEng = -8006.1198 E_bond = 47.1331 E_angle = 140.9769
		E_dihed = 517.5474 E_impro = 5.7244 E_vdwl = 635.2166
		E_coul = 31127.8100 E_long = -40480.5282 Press = -920.9624
		---------------- Step 300 ----- CPU = 2.5246 (sec) ----------------
		TotEng = -7050.0984 KinEng = 1049.7346 Temp = 173.1104
		PotEng = -8099.8330 E_bond = 47.4551 E_angle = 156.5090
		E_dihed = 520.6006 E_impro = 9.4008 E_vdwl = 451.0904
		E_coul = 31202.3817 E_long = -40487.2707 Press = -2352.9550
		---------------- Step 400 ----- CPU = 3.3982 (sec) ----------------
		TotEng = -7050.1671 KinEng = 1099.2465 Temp = 181.2753
		PotEng = -8149.4136 E_bond = 56.6375 E_angle = 164.5897
		E_dihed = 528.8356 E_impro = 8.8390 E_vdwl = 525.0114
		E_coul = 31060.0380 E_long = -40493.3650 Press = -2146.9087
		---------------- Step 500 ----- CPU = 4.2800 (sec) ----------------
		TotEng = -7050.2027 KinEng = 1134.4924 Temp = 187.0877
		PotEng = -8184.6951 E_bond = 53.5903 E_angle = 169.1090
		E_dihed = 522.9488 E_impro = 7.9830 E_vdwl = 496.8404
		E_coul = 31058.9967 E_long = -40494.1633 Press = -2537.1829
		---------------- Step 600 ----- CPU = 5.1548 (sec) ----------------
		TotEng = -7050.1894 KinEng = 1122.6756 Temp = 185.1390
		PotEng = -8172.8649 E_bond = 47.9283 E_angle = 168.7967
		E_dihed = 518.7200 E_impro = 9.2011 E_vdwl = 499.6778
		E_coul = 31076.1916 E_long = -40493.3805 Press = -1939.2216
		---------------- Step 700 ----- CPU = 6.0377 (sec) ----------------
		TotEng = -7050.2850 KinEng = 1154.4452 Temp = 190.3781
		PotEng = -8204.7301 E_bond = 54.3594 E_angle = 183.8772
		E_dihed = 513.0797 E_impro = 9.6842 E_vdwl = 522.0052
		E_coul = 31008.3632 E_long = -40496.0990 Press = -2059.4885
		---------------- Step 800 ----- CPU = 6.9161 (sec) ----------------
		TotEng = -7050.2852 KinEng = 1146.2741 Temp = 189.0306
		PotEng = -8196.5593 E_bond = 48.8126 E_angle = 171.3411
		E_dihed = 525.8682 E_impro = 10.5588 E_vdwl = 538.6905
		E_coul = 31003.8447 E_long = -40495.6752 Press = -1458.5181
		---------------- Step 900 ----- CPU = 7.8101 (sec) ----------------
		TotEng = -7050.3025 KinEng = 1154.2134 Temp = 190.3398
		PotEng = -8204.5159 E_bond = 51.1010 E_angle = 177.9642
		E_dihed = 520.6908 E_impro = 8.9539 E_vdwl = 521.5994
		E_coul = 31012.6307 E_long = -40497.4560 Press = -1683.9131
		---------------- Step 1000 ----- CPU = 8.7313 (sec) ----------------
		TotEng = -7050.3166 KinEng = 1179.9351 Temp = 194.5816
		PotEng = -8230.2517 E_bond = 57.8905 E_angle = 190.1556
		E_dihed = 518.1288 E_impro = 10.0403 E_vdwl = 557.6413
		E_coul = 30933.6472 E_long = -40497.7554 Press = -1643.1247
		Loop time of 8.73139 on 8 procs for 1000 steps with 2833 atoms

		Performance: 9.895 ns/day, 2.425 hours/ns, 114.529 timesteps/s
		99.6% CPU use with 8 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 3.2841 \| 3.856 \| 4.393 \| 17.3 \| 44.16
		Bond \| 0.041216 \| 0.074389 \| 0.11041 \| 7.2 \| 0.85
		Kspace \| 2.8668 \| 3.4354 \| 4.0036 \| 18.9 \| 39.35
		Neigh \| 0.3024 \| 0.30315 \| 0.30402 \| 0.1 \| 3.47
		Comm \| 0.58794 \| 0.60511 \| 0.61362 \| 1.0 \| 6.93
		Output \| 0.010607 \| 0.010696 \| 0.010783 \| 0.0 \| 0.12
		Modify \| 0.40802 \| 0.41482 \| 0.42598 \| 0.8 \| 4.75
		Other \| \| 0.03184 \| \| \| 0.36

		Nlocal: 354.125 ave 390 max 323 min
		Histogram: 2 0 2 0 1 0 0 0 1 2
		Nghost: 7219.12 ave 7453 max 6941 min
		Histogram: 1 1 1 1 0 0 0 0 2 2
		Neighs: 179095 ave 217661 max 144647 min
		Histogram: 1 0 1 1 1 2 1 0 0 1

		Total # of neighbors = 1432758
		Ave neighs/atom = 505.739
		Ave special neighs/atom = 4.67702
		Neighbor list builds = 39
		Dangerous builds = 0
		Total wall time: 0:00:09

tools/ch2lmp/example-cmap/1gb1.pdb

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tools/ch2lmp/example-cmap/1gb1.psf

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