Hi Justin,
Sorry I didn't include all of my md.mdp file, as it is quite long :). I
have included as a reference below. I've taken a look at the log file, but
I'm not really sure what I should be looking for so to identify what is
causing my system to blow up? Should I start with the energies
Hi,
The relevant lines of my script are the following:
line 27: # Run MD and write output to /nas2 disk
line 28: $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
line 29:
line 30: # MDRUN completes: now make the next run file for
rainy...@yahoo.com wrote:
Hi Justin,
Sorry I didn't include all of my md.mdp file, as it is quite long :). I
have included as a reference below. I've taken a look at the log file,
but I'm not really sure what I should be looking for so to identify what
is causing my system to blow up?
rainy...@yahoo.com wrote:
Hi,
The relevant lines of my script are the following:
line 27: # Run MD and write output to /nas2 disk
line 28: $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
line 29:
line 30: # MDRUN completes:
hi,
could you specify the system size?
How many steps did it run before you got the segmentation fault? Try to find
if everything went ok until the segmentation fault by saving log and
trajectories.
amit
On Fri, Nov 13, 2009 at 3:53 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Hi Amit,
My system is quite large, comprising of a molecule, water, and Na+ ions,
summing up to 233863 (!) entities total. Regarding the segmentation fault,
the MD simulation only ran for 2 steps before the system crashed.
Could the size of my system caused it to crash? Also, in my md.log
rainy...@yahoo.com wrote:
Hi Amit,
My system is quite large, comprising of a molecule, water, and Na+ ions,
summing up to 233863 (!) entities total. Regarding the segmentation
fault, the MD simulation only ran for 2 steps before the system crashed.
2 steps? Your original post with
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
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
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
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