[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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