[gmx-users] Segmentation fault - Implicit solvent

Steven Neumann s.neumann08 at gmail.com
Thu Mar 1 23:53:58 CET 2012


On Thu, Mar 1, 2012 at 10:26 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  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> 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>> 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>>__>
>>>
>>>
>>>        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>>__>
>>>
>>>
>>>        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>>> 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

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