[gmx-users] Segmentation fault - Implicit solvent

[Justin A. Lemkul]

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.  You will need to upgrade to 
4.5.5 (serial should work on 4.5.4).

-Justin

-- 
========================================

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

========================================