On 11/5/13 7:37 AM, MUSYOKA THOMMAS wrote:
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.
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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