[gmx-users] topology in local?

[Nicola Staffolani]

just to improve my knowledge in programming: and I can override it by
typing:

GMXLIB="address_of_the_new_topology_in_my_computer"

right?

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
Software Center...


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
>> /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 <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
>>> --
>>> Gromacs Users mailing list
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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
> http://mackerell.umaryland.edu/~jalemkul
>
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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