[gmx-users] topology in local?

[Nicola Staffolani]

and grompp runs quite quickly, that's perfect, much less risky (for such a
clumsy programmer like me!!) than changing the address $GMXLIB is pointing
too (many won't agree on it, I guess ;)

Thank you Justin!!

Nicola


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.
>
> -Justin
>
> --
> ==================================================
>
> 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
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
Nicola Staffolani PhD
Biophysics & Nanoscience Centre CNISM <http://www.unitus.it/biophysics>
Università della Tuscia
Largo dell'Università s.n.c., I-01100 Viterbo
email: n.staffolani at unitus.it
tel.: +39 0761 35 70 27; fax: +39 0761 35 71 36