[gmx-users] Segmentation fault - Implicit solvent

[Steven Neumann]

On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:

>
>
>  On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul <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>.
>>  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?

Steven


>  Steven
>
>
>
>> --
>> ==============================**==========
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
>> --
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>
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