Dear Gromacs users,
I tried to run coarse grained MD however after a few steps I got: Step 39, time 0.78 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.038933, max 2.260527 (between atoms 10459 and 10463) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 10457 10459 89.8 0.3107 0.8288 0.3100 10459 10463 90.3 0.3075 1.0108 0.3100 10463 10467 90.6 0.3084 0.8774 0.3100 10467 10469 81.1 0.3103 0.3823 0.3100 10469 10471 90.3 0.3121 0.1885 0.3100 Wrote pdb files with previous and current coordinates Step 40, time 0.8 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 165002.767686, max 10334958.000000 (between atoms 10457 and 10459) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 10443 10445 30.1 0.3100 0.3581 0.3100 10445 10447 102.2 0.3102 266.6146 0.3100 10447 10450 59.3 0.3100 624.1382 0.3100 10450 10452 101.4 0.3105 5390.4609 0.3100 10452 10454 87.9 0.3083 104154.3047 0.3100 10454 10457 83.9 0.3497 439143.5312 0.3100 10457 10459 87.5 0.8288 3203837.2500 0.3100 10459 10463 87.8 1.0108 2960821.2500 0.3100 10463 10467 95.2 0.8774 763857.8125 0.3100 10467 10469 95.5 0.3823 195859.2656 0.3100 10469 10471 104.3 0.1885 43565.4141 0.3100 10471 10473 90.3 0.3534 7857.3394 0.3100 10473 10475 105.5 0.3125 57.7529 0.3100 10475 10477 90.0 0.3099 0.3849 0.3100 10477 10480 32.4 0.3101 0.3647 0.3100 Wrote pdb files with previous and current coordinates mpiexec: process_obit_event: evt 6 task 0 on wn518 stat 267. mpiexec: wait_tasks: waiting for wn350 wn350 wn501. mpiexec: kill_others_now: alarm went off, killing all other tasks. mpiexec: kill_tasks: killing all tasks. mpiexec: process_kill_event: evt 10 task 1 on wn350. mpiexec: process_kill_event: evt 12 task 3 on wn501. mpiexec: process_kill_event: evt 11 task 2 on wn350. mpiexec: process_obit_event: evt 7 task 3 on wn501 stat 265. mpiexec: process_obit_event: evt 8 task 1 on wn350 stat 265. mpiexec: process_obit_event: evt 9 task 2 on wn350 stat 265. mpiexec: Warning: task 0 died with signal 11 (Segmentation fault). mpiexec: Warning: tasks 1-3 died with signal 9 (Killed). in log file last line is: Constraining the starting coordinates (step 0) Constraining the coordinates at t0-dt (step 0) RMS relative constraint deviation after constraining: 4.04e-06 Initial temperature: 1.8161e-07 K Started mdrun on node 0 Wed Jul 30 10:39:50 2014 Step Time Lambda 0 0.00000 0.00000 Grid: 42 x 42 x 42 cells Energies (kJ/mol) Bond G96Angle Proper Dih. Improper Dih. LJ (SR) 6.24872e+03 1.47844e+04 1.75778e+03 4.11810e+02 -2.32179e+07 Coulomb (SR) Position Rest. Potential Kinetic En. Total Energy -4.49776e+03 2.00073e-01 -2.31992e+07 1.44043e+01 -2.31992e+07 Temperature Pressure (bar) Constr. rmsd 1.55259e-03 -1.41563e+03 5.56533e-06 my input file: define = -DPOSRES dt = 0.02 nsteps = 25000 nstxout = 0 nstvout = 0 nstlog = 100 nstxtcout = 100 xtc-precision = 10 rlist = 1.4 coulombtype = shift rcoulomb = 1.2 epsilon_r = 15 vdw-type = shift rvdw-switch = 0.9 rvdw = 1.2 tcoupl = v-rescale tc-grps = Protein W tau-t = 1.0 1.0 ref-t = 300 300 Pcoupl = Berendsen Pcoupltype = isotropic tau-p = 12.0 compressibility = 3e-4 ref-p = 1.0 refcoord_scaling = com What is wrong here? best regards Urszula Uciechowska ----------------------------------------- Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.