rainy...@yahoo.com wrote:
Hi all,
I've encountered a problem while trying to run Gromacs on my
coarse-grained molecule. I've already performed the initial energy
minimization. I tried to run the inital MD simulation, but the job was
cut short due to a segmentation fault, as mentioned in the output file:
^Mstep 0^Mstep 100, will finish Wed Dec 16 16:55:17 2009^Mstep 200, will
finish Wed Dec 16 07:04:11 2009^Mstep 300, will finish Wed Dec 16
12:59:33 2009^Mstep 400, will finish Wed Dec 16 09:02:03 2009^Mstep 500,
will finish Wed Dec 16 12:12:01 2009^Mstep 600, will finish Wed Dec 16
14:18:47 2009^Mstep 700, will finish Wed Dec 16 15:49:22 2009^Mstep 800,
will finish Wed Dec 16 13:29:16 2009^Mstep 900, will finish Wed Dec 16
14:45:15 2009^Mstep 1000, will finish Wed Dec 16 15:46:03 2009
/opt/gridengine/default/spool/
compute-0-7/job_scripts/182710: line 28: 18851 Segmentation fault
(core dumped) $MDRUN -v -nice 0 -np $NSLOTS -s npg3_4.tpr -o npg3_4.trr
-c confout.gro -g npg3_4.log -x npg3_4.xtc -e npg3_4.edr
/opt/gridengine/default/spool/compute-0-7/job_scripts/182710: line 31:
-s: command not found
Does anyone know what could be causing the problem? Should it be of
interest, my em.mdp is included at the bottom.
Thanks for your help!
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
em.mdp
; VARIOUS PREPROCESSING OPTIONS =
title =
cpp = /lib/cpp
include =
define =
; RUN CONTROL PARAMETERS =
integrator = steep
; start time and timestep in ps =
tinit = 0
dt = 0.02
nsteps = 1000
; ENERGY MINIMIZATION OPTIONS =
;emtol = 0.00001
;emstep = 0.1
;nstcgsteep = 1000
emtol = 10
emstep = 0.01
nstcgsteep = 1000
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
md.mdp
; RUN CONTROL PARAMETERS =
; MARTINI - Most simulations are stable with dt=40 fs,
; some (especially rings) require 20-30 fs.
; The range of time steps used for parametrization
; is 20-40 fs, using smaller time steps is therefore not recommended.
integrator = md
; start time and timestep in ps
tinit = 0
dt = 0.020
;nsteps = 10000 ; initial step
nsteps = 10000000 ; 200 ns @ dt=0.02
; number of steps for center of mass motion removal =
nstcomm = 1
comm-grps =
Is this the entirety of your md.mdp file? If so, all other options will be set
to default, and these may or may not (read: likely will not) be appropriate for
your system. A number of factors can lead to a segmentation fault, but in
generic terms, something became unstable. Check the output - look at the
trajectory to see where things start to fall apart. Helpful messages are
usually printed in the log file as well. Beyond that, please consult the following:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
