shivkumar bale wrote:
Hi Gromacs Users,
when I am trying to run the simulation I am getting the following error:
mpispawn.c:303 Unexpected exit status
Child exited abnormally!
Killing remote processes...DONE
I read about this online and it says that simulation is running out of
memory and it depends upon the grid spacing. It also talks about PP/PME
ratio. But I am not able to figure how to make that changes in the mdp file?
Can you provide a link to the information you found?
PP/PME ratio is either guessed, or explicitly set using mdrun -npme. Assuming
the "grid spacing" you refer to is the PME grid spacing, then the fourierspacing
parameter is what you need to set. Usually a default of 0.12 is reasonable;
yours is set at 0.10.
Also, you shouldn't be using -DFLEXIBLE with the md integrator, see here:
http://lists.gromacs.org/pipermail/gmx-users/2008-October/037571.html
-Justin
title = bilayer
cpp = /lib/cpp
include =
define = -DFLEXIBLE
integrator = md
emstep = 0.1
emtol = 10.0
nstcgsteep = 10
dt = 0.001
nsteps = 2000000
nstxout = 10000
nstvout = 10000
nstlog = 10000
nstenergy = 10000
nstxtcout = 10000
xtc_grps =
energygrps =
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.0
vdw-type = Cut-off
rvdw = 1.0
coulombtype = PME
rcoulomb = 1.0
DispCorr = EnerPres
fourierspacing = 0.1
pme_order = 6
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = yes
tcoupl = Berendsen
tc_grps = system
tau_t = 1.0
ref_t = 300
Pcoupl = Berendsen
Pcoupltype = isotropic
tau_p = 4.0
compressibility = 4.5e-5
ref_p = 1.0
gen_vel = yes
gen_temp = 300
gen_seed = 173529
constraints = none
constraint_algorithm = lincs
lincs_order = 8
lincs_iter = 2
Regards,
Shivkumar Bale
--
========================================
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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