On 11/5/13 7:37 AM, MUSYOKA THOMMAS wrote:
Dear Users,
I am running MD simulations of a protein-ligand system. Sometimes when i do
an mdrun, be it for the energy minimization or during the nvt and npt
equillibration  or the actual md run step, sometimes the output files are
named in a very odd way (strange extensions) e.g em.gro.tprr or md.tpr.cpt,

Can anyone explain the cause of this?

You are issuing the command in a way that you probably don't want. I suspect what you are doing is:

mdrun -deffnm md.tpr

The -deffnm option is for the base file name and should not include an extension. mdrun is only doing what you tell it; you're saying, "all my files are named md.tpr, and you can put whatever the necessary extension is on them."

What you want is:

mdrun -deffnm md



Justin A. Lemkul, Ph.D.
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

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