Sayan Bagchi wrote:
Hello All,
I am having a weird problem and I do not know whether it has to do
anything with Gromacs or the cluster setting I am using.
When I run a MD simulation (on any protein), the job automatically
terminates overnight without an error message. I mean if I start the job
early in the morning it runs longer than if I start the job later in the
day. But it never runs to the desired length mentioned in the .mdp file.
If you are not receiving any error messages from Gromacs, then it is something
your system is doing that is unrelated to mdrun. Contact your system
administrators. Some queues employ systems to purge jobs after a certain amount
of time or even stop all jobs at a certain time of day to allow other jobs to start.
-Justin
I am copying the .mdp file:
-----------------------------------------------------
integrator = md
nsteps = 5000000
dt = 0.002
nstlist = 10
nstcomm = 1
rlist = 1.0
coulombtype = pme
rcoulomb = 1.0
vdw-type = cut-off
rvdw = 1.0
tcoupl = Nose-Hoover
tc-grps = protein non-protein
tau-t = 0.5 0.5
ref-t = 298 298
Pcoupl = Parrinello-Rahman
pcoupltype = isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
nstxout = 100
nstvout = 100
nstxtcout = 100
nstenergy = 100
userint1 = 123
userint2 = 124
userint3 = 247
-----------------------------------------------------------
Any thoughts?
Sayan.
--
========================================
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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