[gmx-users] Segmentation fault - Implicit solvent

Mark Abraham Mark.Abraham at anu.edu.au
Thu Mar 1 23:26:30 CET 2012


On 2/03/2012 9:22 AM, Steven Neumann wrote:
>
>
> On Thu, Mar 1, 2012 at 10:07 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>     Steven Neumann wrote:
>
>
>
>         On Thu, Mar 1, 2012 at 5:43 PM, Justin A. Lemkul
>         <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
>            Steven Neumann wrote:
>
>
>
>                On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann
>         <s.neumann08 at gmail.com <mailto:s.neumann08 at gmail.com>
>         <mailto:s.neumann08 at gmail.com <mailto:s.neumann08 at gmail.com>>
>         <mailto:s.neumann08 at gmail.com <mailto:s.neumann08 at gmail.com>
>         <mailto:s.neumann08 at gmail.com <mailto:s.neumann08 at gmail.com>>>__>
>
>                wrote:
>
>
>
>                   On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann
>         <s.neumann08 at gmail.com <mailto:s.neumann08 at gmail.com>
>         <mailto:s.neumann08 at gmail.com <mailto:s.neumann08 at gmail.com>>
>         <mailto:s.neumann08 at gmail.com <mailto:s.neumann08 at gmail.com>
>         <mailto:s.neumann08 at gmail.com <mailto:s.neumann08 at gmail.com>>>__>
>
>                wrote:
>
>
>
>                       On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul
>         <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at 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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