[gmx-users] topology in local?

Thu May 22 09:42:30 CEST 2014

thank you!

On Wed, May 21, 2014 at 4:10 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/21/14, 9:06 AM, Nicola Staffolani wrote:
>
>> just to improve my knowledge in programming: and I can override it by
>> typing:
>>
>> GMXLIB="address_of_the_new_topology_in_my_computer"
>>
>> right?
>>
>>
> The details depend on your shell.  For csh you need setenv, for bash you
> need export, etc.  Quotes shouldn't be necessary, e.g.:
>
> export GMXLIB=/home/justin/software/gromacs/custom/share/top
>
>
>  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!
>>
>>
> Any new shell you open will need the environment variable to be set again;
> if it's something you need often (or always) set it in .bashrc, .cshrc, etc.
>
> -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
>>>>>
>>>>> * Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>> posting!
>>>>>
>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>> * For (un)subscribe requests visit
>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>  --
>>> ==================================================
>>>
>>> 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
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/
>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>>
>>
>>
>>
> --
> ==================================================
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

-- 
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