LAMMPS (12 Dec 2018) using 1 OpenMP thread(s) per MPI task variable dcdfreq index 50 variable outputname index step6.0_minimization units real boundary p p p newton off pair_style lj/charmmfsw/coul/long 10 12 Switching to CHARMM coulomb energy conversion constant (src/KSPACE/pair_lj_charmmfsw_coul_long.cpp:70) pair_modify mix arithmetic kspace_style pppm 1e-6 atom_style full bond_style harmonic angle_style charmm dihedral_style charmmfsw improper_style harmonic special_bonds charmm timestep 1 read_data step5_charmm2lammps.data Reading data file ... orthogonal box = (-23.8118 -23.8118 -37.58) to (23.8118 23.8118 37.58) 3 by 3 by 4 MPI processor grid reading atoms ... 15840 atoms scanning bonds ... 4 = max bonds/atom scanning angles ... 18 = max angles/atom scanning dihedrals ... 41 = max dihedrals/atom scanning impropers ... 1 = max impropers/atom reading bonds ... 13608 bonds reading angles ... 20160 angles reading dihedrals ... 32832 dihedrals reading impropers ... 144 impropers Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 4 = max # of 1-2 neighbors 12 = max # of 1-3 neighbors 16 = max # of 1-4 neighbors 20 = max # of special neighbors neighbor 2 bin neigh_modify delay 5 every 1 velocity all create 323.15 1394564435 dist gaussian include restraints/constraint_angletype variable constraint_angletype string "37" fix 1 all nvt temp 323.15 323.15 100.0 shell sed -e "s/\$fc/5/g" step5_charmm2lammps.col > restraints/${outputname}.col shell sed -e "s/\$fc/5/g" step5_charmm2lammps.col > restraints/step6.0_minimization.col #fix restraint all colvars restraints/${outputname}.col output ${outputname} shell tr '[A-Z]' '[a-z]' < restraints/dihe.restraint |sed -e "s/\$fc/1.0/g" > restraints/${outputname}.dihe shell tr '[A-Z]' '[a-z]' < restraints/dihe.restraint |sed -e "s/\$fc/1.0/g" > restraints/step6.0_minimization.dihe include restraints/${outputname}.dihe include restraints/step6.0_minimization.dihe fix improp1 all restrain dihedral 36 25 28 30 1.0 1.0 120.0 fix improp2 all restrain dihedral 166 155 158 160 1.0 1.0 120.0 fix improp3 all restrain dihedral 296 285 288 290 1.0 1.0 120.0 fix improp4 all restrain dihedral 426 415 418 420 1.0 1.0 120.0 fix improp5 all restrain dihedral 556 545 548 550 1.0 1.0 120.0 fix improp6 all restrain dihedral 686 675 678 680 1.0 1.0 120.0 fix improp7 all restrain dihedral 816 805 808 810 1.0 1.0 120.0 fix improp8 all restrain dihedral 946 935 938 940 1.0 1.0 120.0 fix improp9 all restrain dihedral 1076 1065 1068 1070 1.0 1.0 120.0 fix improp10 all restrain dihedral 1206 1195 1198 1200 1.0 1.0 120.0 fix improp11 all restrain dihedral 1336 1325 1328 1330 1.0 1.0 120.0 fix improp12 all restrain dihedral 1466 1455 1458 1460 1.0 1.0 120.0 fix improp13 all restrain dihedral 1596 1585 1588 1590 1.0 1.0 120.0 fix improp14 all restrain dihedral 1726 1715 1718 1720 1.0 1.0 120.0 fix improp15 all restrain dihedral 1856 1845 1848 1850 1.0 1.0 120.0 fix improp16 all restrain dihedral 1986 1975 1978 1980 1.0 1.0 120.0 fix improp17 all restrain dihedral 2116 2105 2108 2110 1.0 1.0 120.0 fix improp18 all restrain dihedral 2246 2235 2238 2240 1.0 1.0 120.0 fix improp19 all restrain dihedral 2376 2365 2368 2370 1.0 1.0 120.0 fix improp20 all restrain dihedral 2506 2495 2498 2500 1.0 1.0 120.0 fix improp21 all restrain dihedral 2636 2625 2628 2630 1.0 1.0 120.0 fix improp22 all restrain dihedral 2766 2755 2758 2760 1.0 1.0 120.0 fix improp23 all restrain dihedral 2896 2885 2888 2890 1.0 1.0 120.0 fix improp24 all restrain dihedral 3026 3015 3018 3020 1.0 1.0 120.0 fix improp25 all restrain dihedral 3156 3145 3148 3150 1.0 1.0 120.0 fix improp26 all restrain dihedral 3286 3275 3278 3280 1.0 1.0 120.0 fix improp27 all restrain dihedral 3416 3405 3408 3410 1.0 1.0 120.0 fix improp28 all restrain dihedral 3546 3535 3538 3540 1.0 1.0 120.0 fix improp29 all restrain dihedral 3676 3665 3668 3670 1.0 1.0 120.0 fix improp30 all restrain dihedral 3806 3795 3798 3800 1.0 1.0 120.0 fix improp31 all restrain dihedral 3936 3925 3928 3930 1.0 1.0 120.0 fix improp32 all restrain dihedral 4066 4055 4058 4060 1.0 1.0 120.0 fix improp33 all restrain dihedral 4196 4185 4188 4190 1.0 1.0 120.0 fix improp34 all restrain dihedral 4326 4315 4318 4320 1.0 1.0 120.0 fix improp35 all restrain dihedral 4456 4445 4448 4450 1.0 1.0 120.0 fix improp36 all restrain dihedral 4586 4575 4578 4580 1.0 1.0 120.0 fix improp37 all restrain dihedral 4716 4705 4708 4710 1.0 1.0 120.0 fix improp38 all restrain dihedral 4846 4835 4838 4840 1.0 1.0 120.0 fix improp39 all restrain dihedral 4976 4965 4968 4970 1.0 1.0 120.0 fix improp40 all restrain dihedral 5106 5095 5098 5100 1.0 1.0 120.0 fix improp41 all restrain dihedral 5236 5225 5228 5230 1.0 1.0 120.0 fix improp42 all restrain dihedral 5366 5355 5358 5360 1.0 1.0 120.0 fix improp43 all restrain dihedral 5496 5485 5488 5490 1.0 1.0 120.0 fix improp44 all restrain dihedral 5626 5615 5618 5620 1.0 1.0 120.0 fix improp45 all restrain dihedral 5756 5745 5748 5750 1.0 1.0 120.0 fix improp46 all restrain dihedral 5886 5875 5878 5880 1.0 1.0 120.0 fix improp47 all restrain dihedral 6016 6005 6008 6010 1.0 1.0 120.0 fix improp48 all restrain dihedral 6146 6135 6138 6140 1.0 1.0 120.0 fix improp49 all restrain dihedral 6276 6265 6268 6270 1.0 1.0 120.0 fix improp50 all restrain dihedral 6406 6395 6398 6400 1.0 1.0 120.0 fix improp51 all restrain dihedral 6536 6525 6528 6530 1.0 1.0 120.0 fix improp52 all restrain dihedral 6666 6655 6658 6660 1.0 1.0 120.0 fix improp53 all restrain dihedral 6796 6785 6788 6790 1.0 1.0 120.0 fix improp54 all restrain dihedral 6926 6915 6918 6920 1.0 1.0 120.0 fix improp55 all restrain dihedral 7056 7045 7048 7050 1.0 1.0 120.0 fix improp56 all restrain dihedral 7186 7175 7178 7180 1.0 1.0 120.0 fix improp57 all restrain dihedral 7316 7305 7308 7310 1.0 1.0 120.0 fix improp58 all restrain dihedral 7446 7435 7438 7440 1.0 1.0 120.0 fix improp59 all restrain dihedral 7576 7565 7568 7570 1.0 1.0 120.0 fix improp60 all restrain dihedral 7706 7695 7698 7700 1.0 1.0 120.0 fix improp61 all restrain dihedral 7836 7825 7828 7830 1.0 1.0 120.0 fix improp62 all restrain dihedral 7966 7955 7958 7960 1.0 1.0 120.0 fix improp63 all restrain dihedral 8096 8085 8088 8090 1.0 1.0 120.0 fix improp64 all restrain dihedral 8226 8215 8218 8220 1.0 1.0 120.0 fix improp65 all restrain dihedral 8356 8345 8348 8350 1.0 1.0 120.0 fix improp66 all restrain dihedral 8486 8475 8478 8480 1.0 1.0 120.0 fix improp67 all restrain dihedral 8616 8605 8608 8610 1.0 1.0 120.0 fix improp68 all restrain dihedral 8746 8735 8738 8740 1.0 1.0 120.0 fix improp69 all restrain dihedral 8876 8865 8868 8870 1.0 1.0 120.0 fix improp70 all restrain dihedral 9006 8995 8998 9000 1.0 1.0 120.0 fix improp71 all restrain dihedral 9136 9125 9128 9130 1.0 1.0 120.0 fix improp72 all restrain dihedral 9266 9255 9258 9260 1.0 1.0 120.0 thermo ${dcdfreq} thermo 50 thermo_style custom step time xlo xhi ylo yhi zlo zhi etotal pe ke temp press ebond eangle edihed eimp evdwl ecoul elong temp vol dump 1 all dcd ${dcdfreq} ${outputname}.dcd dump 1 all dcd 50 ${outputname}.dcd dump 1 all dcd 50 step6.0_minimization.dcd dump_modify 1 unwrap yes write_data ${outputname}.data write_data step6.0_minimization.data System init for write_data ... PPPM initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.271993 grid = 48 48 72 stencil order = 5 estimated absolute RMS force accuracy = 0.000362141 estimated relative force accuracy = 1.09055e-06 using double precision FFTs 3d grid and FFT values/proc = 13225 4608 Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 binsize = 7, bins = 7 7 11 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/charmmfsw/coul/long, perpetual attributes: half, newton off pair build: half/bin/newtoff stencil: half/bin/3d/newtoff bin: standard min_style cg minimize 0.0 1.0e-8 10000 20000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) PPPM initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.271993 grid = 48 48 72 stencil order = 5 estimated absolute RMS force accuracy = 0.000362141 estimated relative force accuracy = 1.09055e-06 using double precision FFTs 3d grid and FFT values/proc = 13225 4608 Setting up cg style minimization ... Unit style : real Current step : 0 ERROR on proc 0: Restrain atoms 7186 7175 7178 7180 missing on proc 0 at step 0 (src/fix_restrain.cpp:478) Last command: minimize 0.0 1.0e-8 10000 20000 ERROR on proc 5: Restrain atoms 1206 1195 1198 1200 missing on proc 5 at step 0 (src/fix_restrain.cpp:478) Last command: minimize 0.0 1.0e-8 10000 20000 ERROR on proc 6: Restrain atoms 4586 4575 4578 4580 missing on proc 6 at step 0 (src/fix_restrain.cpp:478) Last command: minimize 0.0 1.0e-8 10000 20000 ERROR on proc 7: Restrain atoms 4586 4575 4578 4580 missing on proc 7 at step 0 (src/fix_restrain.cpp:478) Last command: minimize 0.0 1.0e-8 10000 20000 ERROR on proc 9: Restrain atoms 1206 1195 1198 1200 missing on proc 9 at step 0 (src/fix_restrain.cpp:478) Last command: minimize 0.0 1.0e-8 10000 20000 ERROR on proc 13: Restrain atoms 1206 1195 1198 1200 missing on proc 13 at step 0 (src/fix_restrain.cpp:478) Last command: minimize 0.0 1.0e-8 10000 20000 ERROR on proc 18: Restrain atoms 2636 2625 2628 2630 missing on proc 18 at step 0 (src/fix_restrain.cpp:478) Last command: minimize 0.0 1.0e-8 10000 20000 ERROR on proc 29: Restrain atoms 1206 1195 1198 1200 missing on proc 29 at step 0 (src/fix_restrain.cpp:478) Last command: minimize 0.0 1.0e-8 10000 20000 ERROR on proc 1: Restrain atoms 1206 1195 1198 1200 missing on proc 1 at step 0 (src/fix_restrain.cpp:478) Last command: minimize 0.0 1.0e-8 10000 20000 ERROR on proc 2: Restrain atoms 1466 1455 1458 1460 missing on proc 2 at step 0 (src/fix_restrain.cpp:478) Last command: minimize 0.0 1.0e-8 10000 20000 ERROR on proc 3: Restrain atoms 1466 1455 1458 1460 missing on proc 3 at step 0 (src/fix_restrain.cpp:478) Last command: minimize 0.0 1.0e-8 10000 20000 ERROR on proc 10: Restrain atoms 9006 8995 8998 9000 missing on proc 10 at step 0 (src/fix_restrain.cpp:478) Last command: minimize 0.0 1.0e-8 10000 20000 ERROR on proc 12: Restrain atoms 7186 7175 7178 7180 missing on proc 12 at step 0 (src/fix_restrain.cpp:478) Last command: minimize 0.0 1.0e-8 10000 20000 ERROR on proc 15: Restrain atoms 1466 1455 1458 1460 missing on proc 15 at step 0 (src/fix_restrain.cpp:478) Last command: minimize 0.0 1.0e-8 10000 20000 ERROR on proc 17: Restrain atoms 1206 1195 1198 1200 missing on proc 17 at step 0 (src/fix_restrain.cpp:478) Last command: minimize 0.0 1.0e-8 10000 20000 ERROR on proc 19: Restrain atoms 2636 2625 2628 2630 missing on proc 19 at step 0 (src/fix_restrain.cpp:478) Last command: minimize 0.0 1.0e-8 10000 20000 ERROR on proc 21: Restrain atoms 1206 1195 1198 1200 missing on proc 21 at step 0 (src/fix_restrain.cpp:478) Last command: minimize 0.0 1.0e-8 10000 20000 ERROR on proc 22: Restrain atoms 9006 8995 8998 9000 missing on proc 22 at step 0 (src/fix_restrain.cpp:478) Last command: minimize 0.0 1.0e-8 10000 20000 ERROR on proc 24: Restrain atoms 7186 7175 7178 7180 missing on proc 24 at step 0 (src/fix_restrain.cpp:478) Last command: minimize 0.0 1.0e-8 10000 20000 ERROR on proc 25: Restrain atoms 1206 1195 1198 1200 missing on proc 25 at step 0 (src/fix_restrain.cpp:478) Last command: minimize 0.0 1.0e-8 10000 20000 ERROR on proc 26: Restrain atoms 9006 8995 8998 9000 missing on proc 26 at step 0 (src/fix_restrain.cpp:478) Last command: minimize 0.0 1.0e-8 10000 20000 ERROR on proc 30: Restrain atoms 2636 2625 2628 2630 missing on proc 30 at step 0 (src/fix_restrain.cpp:478) Last command: minimize 0.0 1.0e-8 10000 20000 ERROR on proc 31: Restrain atoms 2636 2625 2628 2630 missing on proc 31 at step 0 (src/fix_restrain.cpp:478) Last command: minimize 0.0 1.0e-8 10000 20000 ERROR on proc 33: Restrain atoms 1206 1195 1198 1200 missing on proc 33 at step 0 (src/fix_restrain.cpp:478) Last command: minimize 0.0 1.0e-8 10000 20000 ERROR on proc 34: Restrain atoms 9006 8995 8998 9000 missing on proc 34 at step 0 (src/fix_restrain.cpp:478) Last command: minimize 0.0 1.0e-8 10000 20000 ERROR on proc 14: Restrain atoms 1466 1455 1458 1460 missing on proc 14 at step 0 (src/fix_restrain.cpp:478) Last command: minimize 0.0 1.0e-8 10000 20000