On 10/13/15 7:28 PM, thomas knitter wrote:
My input files are abc.gro, index.ndx topol.top, minim.mdp. I prepared a script to get the job running module load GROMACS/5.0.4-intel-2015A-mt # gmx grompp -f minim.mdp -c abc.gro -p topol.top -n index.ndx -o em.tpr gmx mdrun -v -deffnm em gmx energy -f em.edr << EOF 9 0 EOF ## I keep getting can not open file: em.tpr file
Then grompp failed, and you need to look in stderr/stdout for the reason why. -Justin -- ================================================== 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
