[gmx-users] topology in local?

[Nicola Staffolani]

and so how do I make GMXLIB point to somewhere else than
/usr/share/gromacs/top?


On Wed, May 21, 2014 at 12:58 PM, Chandan Choudhury <iitdckc at gmail.com>wrote:

> On Wed, May 21, 2014 at 3:57 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?
> >
> Sure.
>
> >
> > 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?
> >
> >
> I do not understand where your confusion lies. BTW, Gromacs works in the
> following way:
> 1. pdb2gmx  generates the topolopy file (human readable).
> 2. grompp reads this topology and the structure file to generate a tpr
> (binary
> file).
> In the process of generating the tpr file, it reads the force field (FF)
> files. The location of the FF is taken from the GMXLIB variable. GMXLIB may
> point to any path of the computer where the FF is kept.
> 3. You can use this tpr file, to run your simulation to which every
> computer you want (gmx should be installed).
> If a simulation is already running, then your simulation would take more
> time to complete. Your tpr file will not be affected by the previous
> simulation.
>
> The same is also told by Justin.
>
> Thank you,
> >
> > Nicola
> >
> > --
> 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