[gmx-users] topology in local?

Chandan Choudhury iitdckc at gmail.com
Wed May 21 12:58:36 CEST 2014

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?

> 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
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

The same is also told by Justin.

Thank you,
> Nicola
> --
Chandan Kumar Choudhury
National Chemical Laboratory, Pune

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