On Thu, Mar 1, 2012 at 10:07 PM, Justin A. Lemkul <[email protected]> wrote:
> > > Steven Neumann wrote: > >> >> >> On Thu, Mar 1, 2012 at 5:43 PM, Justin A. Lemkul <[email protected]<mailto: >> [email protected]>> wrote: >> >> >> >> Steven Neumann wrote: >> >> >> >> On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>**>__> >> >> wrote: >> >> >> >> On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>**>__> >> >> wrote: >> >> >> >> On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[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> >> >> <http://redmine.gromacs.org/__**issues/777<http://redmine.gromacs.org/__issues/777> >> > >> >> >> <http://redmine.gromacs.org/__**issues/777<http://redmine.gromacs.org/__issues/777> >> >> <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 : >> >> >> I think, as stated in the redmine issue cited before, the limit is 2 >> threads/processors. >> >> -Justin >> >> >> >> I tried on one thread and on two threads and the error is still the same. >> Without particle decomposition the problem remains. Any suggestions? >> >> > Then the problem lies outside of the algorithms. Your system has become > instantly unstable, thus suggesting that you have not sufficiently > minimized or equilibrated the structure. > I run the same simulation with cutoff of 2.0 and it works fine. Does it mean I cannot use vdw and coulombic cutoff set to 0? It would be more realistic. Steven > > -Justin > > > -- > ==============================**========== > > 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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