[gmx-users] topology in local?

[Nicola Staffolani]

By the way, if I echo $GMXLIB, I can't see it, but GROMACS is working: is
it OK?


On Wed, May 21, 2014 at 12:27 PM, Nicola Staffolani
<n.staffolani at unitus.it>wrote:

> 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
>> --
>> Gromacs Users mailing list
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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
>



-- 
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