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

Justin Lemkul jalemkul at vt.edu
Fri Jan 6 19:39:48 CET 2017

On 1/5/17 3:40 AM, Aditya Padhi wrote:
> 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.

This usually means the binary is compiled in a manner that is not compatible 
with the target hardware (e.g. the machine where you compiled GROMACS is 
different than the compute node).

> 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.




Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


More information about the gromacs.org_gmx-users mailing list