LAMMPS (22 Jun 2007) ########################## # Initialization #------------------------- units real boundary p p p atom_style full # atom_style atomic #atom_modify map array # default #dimension 3 # default #newton on # default, Newton 3rd Law #processors 2 4 4 # Num. of processors in each dimension #------------------------- # Force field parameters #------------------------- bond_style harmonic angle_style harmonic dihedral_style harmonic improper_style cvff #--------------------------------------- # Non-bond interactions - Ewald - PPPM #--------------------------------------- dielectric 1.0 # default neighbor 4.0 bin # half of the cutoff neigh_modify every 1 delay 1 check yes pair_style lj/cut/coul/long 14.0 14.0 # Global Setting kspace_style pppm 1.0e-6 #kspace_modify order 4 #kspace_modify slab 3.0 # default #--------------------------------- # Non-bond interactions - cutoff #--------------------------------- #dielectric 1 # default #neighbor 2.0 bin # half of the cutoff #neigh_modify every 1 delay 1 check yes #pair_style lj/cut/coul/cut 10.0 14.0 #---------------- # Read geometry #---------------- read_restart 01md.restart.100000 # attention orthogonal box = (0 0 0) to (60.2253 60.2253 60.2253) 2 by 2 by 2 processor grid 21140 atoms 14627 bonds 9582 angles 4473 dihedrals 94 impropers 4 = max # of 1-2 neighbors 12 = max # of 1-3 neighbors 22 = max # of 1-4 neighbors 26 = max # of special neighbors #read_data CBMA_10u_ball_wat.data # attention #--------------------- # initial velocities #--------------------- velocity all create 300.0 4928459 rot yes mom yes dist gaussian #---------------- # Regular fixes #---------------- fix 1 all nvt 300.0 300.0 1.0 # drag 2.0 Resetting global state of Fix 1 Style nvt from restart file info #fix 2 all npt 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0 #---------------- # Deform fixes #---------------- #fix 1 all nvt/sllod 300.0 300.0 100.0 #fix 2 all deform 1 x scale 0.0005 y volume z volume remap v units box #------------------------------- # Customize output infomration #------------------------------- thermo 2000 # output thermodynamics every N timesteps thermo_style multi # custom step temp ke pe ebond eangle edihed eimp evdwl ecoul press vol dump mydump all atom 2000 02md.dump restart 10000 02md.restart #--------------------- # Run a simulation #--------------------- timestep 0.5 # default run 200000 PPPM initialization ... G vector = 0.236277 grid = 54 54 54 RMS precision = 9.88927e-07 brick FFT buffer size/proc = 46656 20412 19440 Memory usage per processor = 43.1341 Mbytes ---------------- Step 100000 ----- CPU = 0.0000 (sec) ---------------- TotEng = -62657.7640 KinEng = 18903.4031 Temp = 300.0000 PotEng = -81561.1671 E_bond = 7036.2550 E_angle = 7227.2831 E_dihed = 386.5797 E_impro = 116.6927 E_vdwl = 18110.7193 E_coul = 199848.0606 E_long = -314286.7576 Press = -553.0619 ---------------- Step 102000 ----- CPU = 812.7809 (sec) ---------------- TotEng = -58451.3319 KinEng = 16667.6037 Temp = 264.5175 PotEng = -75118.9356 E_bond = 7216.5749 E_angle = 7503.1994 E_dihed = 361.3648 E_impro = 96.4242 E_vdwl = 16127.2285 E_coul = 207855.7126 E_long = -314279.4400 Press = 270.1082 ---------------- Step 104000 ----- CPU = 1649.3103 (sec) ---------------- TotEng = -54768.5009 KinEng = 18740.3319 Temp = 297.4120 PotEng = -73508.8328 E_bond = 7369.3350 E_angle = 8511.8470 E_dihed = 371.0157 E_impro = 101.2880 E_vdwl = 16177.7917 E_coul = 208214.0078 E_long = -314254.1179 Press = 1072.8700 ---------------- Step 106000 ----- CPU = 2484.1829 (sec) ---------------- TotEng = -54499.7761 KinEng = 18276.7812 Temp = 290.0554 PotEng = -72776.5573 E_bond = 7753.2138 E_angle = 8405.0783 E_dihed = 432.0335 E_impro = 119.4634 E_vdwl = 16033.5610 E_coul = 208726.6183 E_long = -314246.5255 Press = -348.7614 ---------------- Step 108000 ----- CPU = 3263.1078 (sec) ---------------- TotEng = -53958.7300 KinEng = 18780.7142 Temp = 298.0529 PotEng = -72739.4442 E_bond = 6958.5195 E_angle = 8524.2401 E_dihed = 433.4177 E_impro = 161.4843 E_vdwl = 15519.9394 E_coul = 209912.9489 E_long = -314249.9941 Press = -705.9069 ---------------- Step 110000 ----- CPU = 4021.6080 (sec) ---------------- TotEng = -52510.5275 KinEng = 19505.9766 Temp = 309.5629 PotEng = -72016.5041 E_bond = 7339.6139 E_angle = 8225.4118 E_dihed = 402.4929 E_impro = 110.0578 E_vdwl = 15276.1293 E_coul = 210881.0374 E_long = -314251.2472 Press = -909.8147 ---------------- Step 112000 ----- CPU = 4855.8553 (sec) ---------------- TotEng = -56547.0982 KinEng = 16422.6118 Temp = 260.6295 PotEng = -72969.7101 E_bond = 8186.8532 E_angle = 7770.8606 E_dihed = 386.8513 E_impro = 112.7738 E_vdwl = 15567.0473 E_coul = 209270.6967 E_long = -314264.7929 Press = -1636.5667 ---------------- Step 114000 ----- CPU = 5659.6944 (sec) ---------------- TotEng = -55841.9056 KinEng = 16590.4180 Temp = 263.2926 PotEng = -72432.3235 E_bond = 7510.8980 E_angle = 8267.0510 E_dihed = 422.6706 E_impro = 139.4760 E_vdwl = 15552.5309 E_coul = 209909.3349 E_long = -314234.2851 Press = -1988.0078 ---------------- Step 116000 ----- CPU = 6407.9127 (sec) ---------------- TotEng = -53810.0667 KinEng = 17921.0522 Temp = 284.4099 PotEng = -71731.1189 E_bond = 7451.5142 E_angle = 8064.8555 E_dihed = 440.2694 E_impro = 95.9210 E_vdwl = 15286.1505 E_coul = 211169.8887 E_long = -314239.7181 Press = -980.1061 ---------------- Step 118000 ----- CPU = 7157.5401 (sec) ---------------- TotEng = -52470.3589 KinEng = 19591.2692 Temp = 310.9165 PotEng = -72061.6281 E_bond = 7145.4118 E_angle = 7610.1704 E_dihed = 395.1555 E_impro = 107.2765 E_vdwl = 15167.6833 E_coul = 211736.7691 E_long = -314224.0946 Press = -638.7132