On 5/21/14, 9:06 AM, Nicola Staffolani wrote:
just to improve my knowledge in programming: and I can override it by
typing:
GMXLIB="address_of_the_new_topology_in_my_computer"
right?
The details depend on your shell. For csh you need setenv, for bash you need
export, etc. Quotes shouldn't be necessary, e.g.:
export GMXLIB=/home/justin/software/gromacs/custom/share/top
But in that case, if I first open a child shell, then the change will be
effective only there, and as soon as I come back to the parent shell,
GMXLIB will be pointing to the old /usr/share/... address, right?
Thank you Justin!
Any new shell you open will need the environment variable to be set again; if
it's something you need often (or always) set it in .bashrc, .cshrc, etc.
-Justin
PS I do not think I will try to override it anyway ;) And yes, I manually
installed GROMACS because I didn't know I could do it by just using Ubuntu
Software Center...
On Wed, May 21, 2014 at 2:41 PM, Justin Lemkul <jalem...@vt.edu> wrote:
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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==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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