On 2/03/2012 9:22 AM, Steven Neumann wrote:
On Thu, Mar 1, 2012 at 10:07 PM, Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>> wrote:Steven Neumann wrote: On Thu, Mar 1, 2012 at 5:43 PM, Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: Steven Neumann wrote: On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann <s.neuman...@gmail.com <mailto:s.neuman...@gmail.com> <mailto:s.neuman...@gmail.com <mailto:s.neuman...@gmail.com>> <mailto:s.neuman...@gmail.com <mailto:s.neuman...@gmail.com> <mailto:s.neuman...@gmail.com <mailto:s.neuman...@gmail.com>>>__> wrote: On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann <s.neuman...@gmail.com <mailto:s.neuman...@gmail.com> <mailto:s.neuman...@gmail.com <mailto:s.neuman...@gmail.com>> <mailto:s.neuman...@gmail.com <mailto:s.neuman...@gmail.com> <mailto:s.neuman...@gmail.com <mailto:s.neuman...@gmail.com>>>__> wrote: On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu <mailto: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> <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
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