[gmx-users] MDRUN error message

Justin Lemkul jalemkul at vt.edu
Thu Jul 10 14:29:33 CEST 2014

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 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

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


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