[gmx-users] topology in local?

[Justin Lemkul]

On 5/21/14, 7:34 AM, Nicola Staffolani wrote:
> By the way, if I echo $GMXLIB, I can't see it, but GROMACS is working: is
> it OK?
>

Yes, that just suggests you've manually configured your path and library setup 
rather than sourcing GMXRC (which magically sorts everything out for you and 
sets environment variables).

-Justin

>
> On Wed, May 21, 2014 at 12:27 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 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?
>>
>> Thank you,
>>
>> Nicola
>>
>>
>> On Wed, May 21, 2014 at 11:37 AM, Chandan Choudhury <iitdckc at gmail.com>wrote:
>>
>>> Dear Nicola,
>>>
>>> Any number of users can use the top directory, with the choice of his/her
>>> force field.
>>> If anyone wants to edit the top files, then he can copy the top directory
>>> to somewhere and use the GMXLIB variable.
>>>
>>> You can use the GMXLIB environment variable, and point your top
>>> directory's
>>> path to it. For more details  refer
>>> http://www.gromacs.org/Documentation/Terminology/Environment_Variables.
>>>
>>> Chandan
>>>
>>>
>>> On Wed, May 21, 2014 at 2:52 PM, Nicola Staffolani
>>> <n.staffolani at unitus.it>wrote:
>>>
>>>> Dear GROMACS user community,
>>>>
>>>> I have the following problem: I would like to let a simulation run on a
>>>> computer where another simulation, prepared by another user, is already
>>>> running; my simulation and the simulation of the other user need
>>> different
>>>> topologies (I mean, for example, the files ffbonded.itp and
>>> ffnonbonded.itp
>>>> files stored in /usr/share/gromacs/top/forcefield.ff are different; or,
>>> to
>>>> make things more clear, let's suppose as a condition that user 1 needs
>>> to
>>>> use charmm27.ff and user 2 gromos43a1.ff). Does anybody know of any
>>>> solution where the number of computers is kept constant? What would
>>> happen,
>>>> for example, if I would put my topology files inside my local working
>>>> directory?
>>>>
>>>> Thank you very much in advance,
>>>>
>>>> ​Nicola​
>>>>
>>>> --
>>>> 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
>>>> --
>>>> Gromacs Users mailing list
>>>>
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>>>
>>>
>>>
>>> --
>>>
>>> --
>>> Chandan Kumar Choudhury
>>> National Chemical Laboratory, Pune
>>> India
>>> --
>>> Gromacs Users mailing list
>>>
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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
>>
>
>
>

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

==================================================