[gmx-users] Segmentation fault - Implicit solvent

[Steven Neumann]

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?

thank you

Steven
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