How should I correct the input file? Urszula Uciechowska > > > On 7/31/14, 7:42 AM, Urszula Uciechowska wrote: >> 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? >> > > Likely this: > > Initial temperature: 1.8161e-07 K > > You haven't generated any velocities, so your system is effectively > frozen, and > you're simultaneously applying a thermostat and barostat, which probably > cause > your velocities to go absolutely insane, blowing up the system. > > Generate velocities at the desired temperature and equilibrate gently. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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. > >
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