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