[gmx-users] topology in local?

[Nicola Staffolani]

Dear Chandan,

thank you for your reply. Anyway, before making any change to my GROMACS
and therefore risking  to "destroy", can I ask again your advice?

>From what I have read about environment
variables<http://en.wikipedia.org/wiki/Environment_variable#Unix>,
if another simulation is already running on a computer and I want to launch
my simulation but using a different topology, and if my new topology is
stored in the directory somewhere/my_topology, then I should send the
following command (for example for a md.com command):

$GMXLIB=somewhere/my_topology md.com

Right?

And is it true that the by doing so, I will affect only this simulation,
i.e. I will have changed the path to the topology only for this run, while
for all the next ones the old path (/usr/share/gromacs/top) will be kept?

Thank you,

Nicola


On Wed, May 21, 2014 at 11:37 AM, Chandan Choudhury <iitdckc at gmail.com>wrote:

> Dear Nicola,
>
> Any number of users can use the top directory, with the choice of his/her
> force field.
> If anyone wants to edit the top files, then he can copy the top directory
> to somewhere and use the GMXLIB variable.
>
> You can use the GMXLIB environment variable, and point your top directory's
> path to it. For more details  refer
> http://www.gromacs.org/Documentation/Terminology/Environment_Variables.
>
> Chandan
>
>
> On Wed, May 21, 2014 at 2:52 PM, Nicola Staffolani
> <n.staffolani at unitus.it>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?
> >
> > Thank you very much in advance,
> >
> > ​Nicola​
> >
> > --
> > 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
> > --
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>
> --
>
> --
> Chandan Kumar Choudhury
> National Chemical Laboratory, Pune
> India
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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