[gmx-users] Index file group selection and gmx covar error

Aditya Padhi adi.uoh at gmail.com
Thu Jan 5 09:41:07 CET 2017

Dear Gromacs users,

I am trying to evaluate entropic contributions for a protein-protein
complex using the gmx covar module and then gmx anaeig. When I directly run
the command "gmx covar -f prod.xtc -s prod.tpr -n index.ndx -o eigenval.xvg
-v eigenval.trr -av average.pdb -l covar.log", the program runs and
produces the output. However, when I try to submit it into a node having 16
cores, it shows "Illegal instruction" error and it doesn't run.

In addition, when I use "qsub" to submit the job into the particular node,
it tries to run but eventually I get an error "Fatal error: No input files
(structure or index)". I was wondering if there is any way to specify my
group selection (for e.g. 18 and 19) directly in my input.sh file when I
submit using qsub and is it sufficient to make this run successful? Or the
problem is something related to the pre-compiled binaries.

If anyone can suggest a solution to this issue, it would be really helpful.


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