On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann <s.neuman...@gmail.com>wrote:
> > > On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann <s.neuman...@gmail.com>wrote: > >> >> >> On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul <jalem...@vt.edu>wrote: >> >>> >>> >>> Steven Neumann wrote: >>> >>>> Dear Gmx Users, >>>> I am trying to run nvt simulation (equilibration) of the protein in >>>> implicit solvent. My mdp: >>>> >>>> integrator = md ; leap-frog integrator >>>> >>>> nsteps = 1000000 ; 0.0005 * 1000000 = 0.5 ns >>>> >>>> dt = 0.0005 ; 0.5 fs >>>> >>>> ; Output control >>>> >>>> nstxout = 10000 >>>> >>>> nstxtcout = 10000 ; xtc compressed trajectory output every 2 ps >>>> >>>> nstenergy = 10000 ; save energies every 2 ps >>>> >>>> nstlog = 10000 ; update log file every 2 ps >>>> >>>> ; Bond parameters >>>> >>>> continuation = no >>>> >>>> constraints = none >>>> >>>> ; Neighborsearching >>>> >>>> ns_type = simple ; search neighboring grid cells >>>> >>>> nstlist = 0 ; 10 fs >>>> >>>> rlist = 0 ; short-range neighborlist cutoff (in nm) >>>> >>>> ; Infinite box with no cutoffs >>>> >>>> pbc = no >>>> >>>> rcoulomb = 0 ; short-range electrostatic cutoff (in nm) >>>> >>>> coulombtype = cut-off >>>> >>>> vdwtype = cut-off >>>> >>>> rvdw = 0 ; short-range van der Waals cutoff (in nm) >>>> >>>> epsilon_rf = 0 >>>> >>>> comm_mode = angular ; remove angular and com motions >>>> >>>> ; implicit solvent >>>> >>>> implicit_solvent = GBSA >>>> >>>> gb_algorithm = OBC >>>> >>>> gb_epsilon_solvent = 80.0 >>>> >>>> sa_surface_tension = 2.25936 >>>> >>>> rgbradii = 0 >>>> >>>> sa_algorithm = Ace-approximation >>>> >>>> nstgbradii = 1 >>>> >>>> ; Temperature coupling is on >>>> >>>> Tcoupl = v-rescale >>>> >>>> tau_t = 0.1 >>>> >>>> tc_grps = system >>>> >>>> ref_t = 298 >>>> >>>> ; Velocity generation >>>> >>>> gen_vel = yes ; Velocity generation is on >>>> >>>> gen_temp = 298.0 >>>> >>>> gen_seed = -1 >>>> >>>> Then after grompp I am trying to run the simulation on the cluster: >>>> >>>> mdrun -pd -deffnm nvt500ps >>>> >>>> My log file: >>>> >>>> Back Off! I just backed up nvt500ps.log to ./#nvt500ps.log.1# >>>> >>>> Reading file nvt500ps.tpr, VERSION 4.5.4 (single precision) >>>> >>>> Starting 8 threads >>>> >>>> Back Off! I just backed up nvt500ps.trr to ./#nvt500ps.trr.1# >>>> >>>> Back Off! I just backed up nvt500ps.xtc to ./#nvt500ps.xtc.1# >>>> >>>> Back Off! I just backed up nvt500ps.edr to ./#nvt500ps.edr.1# >>>> >>>> starting mdrun 'Protein' >>>> >>>> 1000000 steps, 500.0 ps. >>>> >>>> Segmentation fault >>>> >>>> >>>> Do you have any clue what is happening? >>>> >>>> >>> Try running in serial or with a maximum of 2 threads. Your problem >>> could be related to >>> http://redmine.gromacs.org/**issues/777<http://redmine.gromacs.org/issues/777>. >>> You will need to upgrade to 4.5.5 (serial should work on 4.5.4). >>> >>> -Justin >>> >>> >> Thank you. What do you mean by running in serial? Well... with 2 threads >> it does not make sense to use implicit solvent. Will 4.5.5 resolve this >> problem? >> >> > > Indeed, it works in serial. Will version 4.5.5 resolve it run it on e.g. > 12 nodes? > > Sorry, the same problem : Initial temperature: 298.398 K Started mdrun on node 0 Thu Mar 1 15:56:04 2012 Step Time Lambda 0 0.00000 0.00000 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 2.27391e+02 4.27461e+02 1.27733e+03 2.73432e+01 -6.95645e+02 GB Polarization Nonpolar Sol. LJ-14 Coulomb-14 LJ (SR) inf 3.59121e+02 6.85627e+02 3.68572e+04 -7.57140e+02 Coulomb (SR) Potential Kinetic En. Total Energy Conserved En. -3.30643e+04 inf nan nan nan Temperature Pressure (bar) nan 0.00000e+00 > > - > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > >
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