[gmx-users] topology in local?
jalemkul at vt.edu
Wed May 21 14:48:53 CEST 2014
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>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?
>>> 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 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
>> 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,
>> 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
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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