[gmx-users] topology in local?

Justin Lemkul 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
> /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.


> 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?
>> 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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