[gmx-users] topology in local?

Justin Lemkul jalemkul at vt.edu
Wed May 21 12:02:36 CEST 2014

On 5/21/14, 5:22 AM, Nicola Staffolani wrote:
> Dear GROMACS user community,
> I have the following problem: I would like to let a simulation run on a
> computer where another simulation, prepared by another user, is already
> running; my simulation and the simulation of the other user need different
> topologies (I mean, for example, the files ffbonded.itp and ffnonbonded.itp
> files stored in /usr/share/gromacs/top/forcefield.ff are different; or, to
> make things more clear, let's suppose as a condition that user 1 needs to
> use charmm27.ff and user 2 gromos43a1.ff). Does anybody know of any
> solution where the number of computers is kept constant? What would happen,
> for example, if I would put my topology files inside my local working
> directory?

Once grompp is invoked, the force field files in $GMXLIB (or anywhere else, for 
that matter) are irrelevant; everything mdrun needs is in the .tpr file.



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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