[gmx-users] Segmentation fault - Implicit solvent

[Steven Neumann]

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?

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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