On Thu, Mar 1, 2012 at 10:26 PM, Mark Abraham <[email protected]>wrote:
> On 2/03/2012 9:22 AM, Steven Neumann wrote: > > > > 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>>. 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. > > > Thus you have an unstable initial system, and can get lucky under some > conditions. Follow the advice here to explore how you can increase the > chance of being lucky under your desired conditions: > http://www.gromacs.org/Documentation/Terminology/Blowing_Up. Or use the > end point of the rc=2.0 simulation as input for one with rc=0. > > Mark > > Thank you Mark! Steven > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > 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 >
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