[gmx-users] topology in local?

Mark Abraham mark.j.abraham at gmail.com
Wed May 21 21:42:18 CEST 2014

On Wed, May 21, 2014 at 12:00 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 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.

/nitpick If using tabulated interactions, those need to be supplied to
mdrun as well. But we'd like to (find time to) put them into the .tpr, too.
The objective is that you should be able to construct the .tpr on your
local machine and have it run "the same" on any machine in the world.


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