On 7/10/14, 12:15 AM, Andy Chao wrote:
Dear GROMACS Users: I used the grompp command to run energy minimization of an ionic liquid structure according to the following command: grompp -f em.mdp -c C4mimNTf2.gro -p C4mimNTf2.top -o NPT.tpr and then run molecular dynamics simulation as the following: mdrun -s NPT.tpr -o NPT.trr when I opend the NPT.trr file, there is nothing inside. Can you explain what was wrong? The last part of the md.log file shows Initialized non-bonded Ewald correction tables, spacing: 6.26e-04 size: 3836 Pinning threads with an auto-selected logical core stride of 1 Initializing LinNear Constraints Solver
Looks like the run never started. Do other simulations proceed? -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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.
