[gmx-users] topology in local?
n.staffolani at unitus.it
Wed May 21 16:04:11 CEST 2014
just to improve my knowledge in programming: and I can override it by
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!
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
On Wed, May 21, 2014 at 2:41 PM, Justin Lemkul <jalemkul at 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
> 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.
>> On Wed, May 21, 2014 at 12:58 PM, Chandan Choudhury <iitdckc at gmail.com
>> 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
>>>> if another simulation is already running on a computer and I want to
>>>> 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
>>>> 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,
>>>> for all the next ones the old path (/usr/share/gromacs/top) will be
>>>> I do not understand where your confusion lies. BTW, Gromacs works in
>>> following way:
>>> 1. pdb2gmx generates the topolopy file (human readable).
>>> 2. grompp reads this topology and the structure file to generate a tpr
>>> 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
>>> 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,
>>> Chandan Kumar Choudhury
>>> National Chemical Laboratory, Pune
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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
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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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
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