On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann <[email protected]>wrote:
> > > On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul <[email protected]> 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? Steven > Steven > > > >> -- >> ==============================**========== >> >> 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 [email protected] >> 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 [email protected]. >> Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >
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