On 5/21/14, 8:38 AM, Nicola Staffolani wrote:
and so how do I make GMXLIB point to somewhere else than
/usr/share/gromacs/top?
If Gromacs is installed in /usr/share/gromacs, that's where it should point.
Otherwise, just override it by setting $GMXLIB in your shell however you like.
Hopefully it won't break anything by doing that.
-Justin
On Wed, May 21, 2014 at 12:58 PM, Chandan Choudhury <iitd...@gmail.com>wrote:
On Wed, May 21, 2014 at 3:57 PM, Nicola Staffolani
<n.staffol...@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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