git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13470 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -1,177 +0,0 @@
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LAMMPS (1 Feb 2014)
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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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orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
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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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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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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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fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
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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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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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G vector (1/distance) = 0.268725
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grid = 15 15 15
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0228209
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estimated relative force accuracy = 6.87243e-05
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using double precision FFTs
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3d grid and FFT values/proc = 10648 3375
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SHAKE stats (type/ave/delta) on step 0
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4 1.111 1.44264e-05
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6 0.996998 7.26967e-06
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8 1.08 1.32536e-05
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10 1.111 1.22749e-05
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12 1.08 1.11767e-05
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14 0.96 0
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18 0.957206 4.37979e-05
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31 104.519 0.00396029
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Memory usage per processor = 22.9109 Mbytes
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---------------- Step 0 ----- CPU = 0.0000 (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 = -845.4774
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---------------- Step 50 ----- CPU = 0.9759 (sec) ----------------
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TotEng = -5247.5490 KinEng = 1132.4011 Temp = 281.4748
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PotEng = -6379.9501 E_bond = 12.2118 E_angle = 31.7365
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E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1771
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E_coul = 26804.4490 E_long = -33907.7002 Press = -1331.7981
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SHAKE stats (type/ave/delta) on step 100
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4 1.111 7.80799e-07
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6 0.997 1.06209e-06
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8 1.08 6.20484e-07
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10 1.111 6.23445e-07
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12 1.08 2.68063e-07
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14 0.96 0
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18 0.957201 5.38018e-06
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31 104.52 0.000502316
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---------------- Step 100 ----- CPU = 1.9636 (sec) ----------------
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TotEng = -5257.9973 KinEng = 1078.0556 Temp = 267.9664
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PotEng = -6336.0529 E_bond = 14.4828 E_angle = 43.4429
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E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3266
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E_coul = 26786.6840 E_long = -33906.5620 Press = -648.6639
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---------------- Step 150 ----- CPU = 2.9816 (sec) ----------------
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TotEng = -5287.2844 KinEng = 1098.6036 Temp = 273.0739
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PotEng = -6385.8881 E_bond = 17.4924 E_angle = 32.8593
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E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9685
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E_coul = 26717.2584 E_long = -33907.2812 Press = -333.1895
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SHAKE stats (type/ave/delta) on step 200
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4 1.111 2.18836e-07
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6 0.997 1.50856e-07
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8 1.08 6.58343e-08
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10 1.111 5.55349e-07
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12 1.08 1.99243e-07
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14 0.96 0
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18 0.957201 3.59666e-06
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31 104.52 0.000388184
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---------------- Step 200 ----- CPU = 3.9551 (sec) ----------------
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TotEng = -5308.4528 KinEng = 1100.5056 Temp = 273.5467
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PotEng = -6408.9584 E_bond = 18.2714 E_angle = 33.3035
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E_dihed = 16.8150 E_impro = 2.6053 E_vdwl = 686.3261
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E_coul = 26736.1131 E_long = -33902.3928 Press = -1470.3871
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---------------- Step 250 ----- CPU = 4.9818 (sec) ----------------
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TotEng = -5294.1808 KinEng = 1071.1623 Temp = 266.2530
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PotEng = -6365.3431 E_bond = 14.2022 E_angle = 39.1953
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E_dihed = 19.4555 E_impro = 3.1387 E_vdwl = 753.5411
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E_coul = 26713.8466 E_long = -33908.7226 Press = -188.8083
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SHAKE stats (type/ave/delta) on step 300
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4 1.111 3.78266e-06
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6 0.997001 3.50137e-06
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8 1.08 2.09323e-06
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10 1.111 5.64331e-06
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12 1.08 2.10401e-06
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14 0.96 0
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18 0.957202 7.67992e-06
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31 104.52 0.000806336
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---------------- Step 300 ----- CPU = 6.0094 (sec) ----------------
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TotEng = -5251.4349 KinEng = 1123.6255 Temp = 279.2934
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PotEng = -6375.0604 E_bond = 14.2249 E_angle = 38.4712
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E_dihed = 18.1324 E_impro = 2.3700 E_vdwl = 715.4556
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E_coul = 26745.4104 E_long = -33909.1249 Press = -469.5456
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Loop time of 6.00943 on 1 procs for 300 steps with 2004 atoms
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Pair time (%) = 4.59488 (76.4612)
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Bond time (%) = 0.0122511 (0.203865)
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Kspce time (%) = 0.654233 (10.8868)
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Neigh time (%) = 0.642603 (10.6932)
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Comm time (%) = 0.0338275 (0.562907)
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Outpt time (%) = 0.000135899 (0.00226142)
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Other time (%) = 0.0715001 (1.1898)
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FFT time (% of Kspce) = 0.0813602 (12.436)
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FFT Gflps 3d (1d only) = 2.02205 3.15151
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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: 11181 ave 11181 max 11181 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 708028 ave 708028 max 708028 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 708028
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Ave neighs/atom = 353.307
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Ave special neighs/atom = 2.34032
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Neighbor list builds = 26
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Dangerous builds = 0
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@ -1,177 +0,0 @@
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LAMMPS (1 Feb 2014)
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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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orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
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1 by 2 by 2 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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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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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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fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
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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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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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G vector (1/distance) = 0.268725
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grid = 15 15 15
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0228209
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estimated relative force accuracy = 6.87243e-05
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using double precision FFTs
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3d grid and FFT values/proc = 4312 960
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SHAKE stats (type/ave/delta) on step 0
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4 1.111 1.44264e-05
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6 0.996998 7.26967e-06
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8 1.08 1.32536e-05
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10 1.111 1.22749e-05
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12 1.08 1.11767e-05
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14 0.96 0
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18 0.957206 4.37979e-05
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31 104.519 0.00396029
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Memory usage per processor = 10.3307 Mbytes
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---------------- Step 0 ----- CPU = 0.0000 (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 = -845.4774
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---------------- Step 50 ----- CPU = 0.2818 (sec) ----------------
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TotEng = -5247.5490 KinEng = 1132.4011 Temp = 281.4748
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PotEng = -6379.9501 E_bond = 12.2118 E_angle = 31.7365
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E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1771
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E_coul = 26804.4490 E_long = -33907.7002 Press = -1331.7981
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SHAKE stats (type/ave/delta) on step 100
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4 1.111 7.80799e-07
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6 0.997 1.06209e-06
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8 1.08 6.20484e-07
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10 1.111 6.23445e-07
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12 1.08 2.68063e-07
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14 0.96 0
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18 0.957201 5.38018e-06
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31 104.52 0.000502316
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---------------- Step 100 ----- CPU = 0.5690 (sec) ----------------
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TotEng = -5257.9973 KinEng = 1078.0556 Temp = 267.9664
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PotEng = -6336.0529 E_bond = 14.4828 E_angle = 43.4429
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E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3266
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E_coul = 26786.6840 E_long = -33906.5620 Press = -648.6639
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---------------- Step 150 ----- CPU = 0.8614 (sec) ----------------
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TotEng = -5287.2845 KinEng = 1098.6036 Temp = 273.0739
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PotEng = -6385.8881 E_bond = 17.4924 E_angle = 32.8593
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E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9685
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E_coul = 26717.2583 E_long = -33907.2812 Press = -333.1895
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SHAKE stats (type/ave/delta) on step 200
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4 1.111 2.18836e-07
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6 0.997 1.50856e-07
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8 1.08 6.58343e-08
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10 1.111 5.55349e-07
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12 1.08 1.99243e-07
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14 0.96 0
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18 0.957201 3.59666e-06
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31 104.52 0.000388184
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---------------- Step 200 ----- CPU = 1.1337 (sec) ----------------
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TotEng = -5308.4528 KinEng = 1100.5056 Temp = 273.5467
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PotEng = -6408.9584 E_bond = 18.2714 E_angle = 33.3035
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E_dihed = 16.8150 E_impro = 2.6053 E_vdwl = 686.3261
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E_coul = 26736.1131 E_long = -33902.3928 Press = -1470.3869
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---------------- Step 250 ----- CPU = 1.4284 (sec) ----------------
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TotEng = -5294.1808 KinEng = 1071.1623 Temp = 266.2530
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PotEng = -6365.3431 E_bond = 14.2022 E_angle = 39.1953
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E_dihed = 19.4555 E_impro = 3.1387 E_vdwl = 753.5412
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E_coul = 26713.8465 E_long = -33908.7226 Press = -188.8075
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SHAKE stats (type/ave/delta) on step 300
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4 1.111 3.78266e-06
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6 0.997001 3.50139e-06
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8 1.08 2.09322e-06
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10 1.111 5.6433e-06
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12 1.08 2.10401e-06
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14 0.96 0
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18 0.957202 7.6799e-06
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31 104.52 0.000806335
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---------------- Step 300 ----- CPU = 1.7292 (sec) ----------------
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TotEng = -5251.4350 KinEng = 1123.6255 Temp = 279.2935
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PotEng = -6375.0605 E_bond = 14.2249 E_angle = 38.4712
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E_dihed = 18.1324 E_impro = 2.3700 E_vdwl = 715.4558
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E_coul = 26745.4101 E_long = -33909.1248 Press = -469.5428
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Loop time of 1.72924 on 4 procs for 300 steps with 2004 atoms
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Pair time (%) = 1.18646 (68.6113)
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Bond time (%) = 0.0033986 (0.196537)
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Kspce time (%) = 0.24268 (14.0339)
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Neigh time (%) = 0.165521 (9.5719)
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Comm time (%) = 0.0693463 (4.01021)
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Outpt time (%) = 0.000285089 (0.0164864)
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Other time (%) = 0.0615544 (3.55962)
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FFT time (% of Kspce) = 0.0323979 (13.35)
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FFT Gflps 3d (1d only) = 5.07792 11.9536
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Nlocal: 501 ave 508 max 490 min
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Histogram: 1 0 0 0 0 0 1 1 0 1
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Nghost: 6586.25 ave 6628 max 6548 min
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Histogram: 1 0 1 0 0 0 1 0 0 1
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Neighs: 177007 ave 180562 max 170212 min
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Histogram: 1 0 0 0 0 0 0 1 1 1
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Total # of neighbors = 708028
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Ave neighs/atom = 353.307
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Ave special neighs/atom = 2.34032
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Neighbor list builds = 26
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Dangerous builds = 0
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Reference in New Issue
Block a user