[gmx-users] Regarding reading .gro file in python

[Dilip H N]

Thank you Justin Sir..

 Yes this is what i wanted..the source code in gromacs..where is the source
written..?? whr/in which files will i be able to get it..??

Thank you



  <https://mailtrack.io/> Sent with Mailtrack
<https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dilip@nitk.edu.in&idSignature=22>
<#>

On Thu, Apr 27, 2017 at 11:56 PM, Dilip H N <cy16f01.dilip at nitk.edu.in>
wrote:

> and how are the x,y,z coordinates, velocities assigned with the values..??
> the logic behind them in gromacs
>
> Thank you
>
>
>
>   <https://mailtrack.io/> Sent with Mailtrack
> <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dilip@nitk.edu.in&idSignature=22>
>
> On Thu, Apr 27, 2017 at 11:52 PM, Dilip H N <cy16f01.dilip at nitk.edu.in>
> wrote:
>
>> Thank you Oliver Beckstein Sir, Dawid das Sir,
>>
>> My questions are..
>>
>> 1] I got the initial configuration of a molecule in .pdb format and thn i
>> gave the command
>> gmx editconf -f .pdb -o box.gro -c -box x y z
>> what happens in the background when this command is given..?? (the C++
>> program runs in which gromacs is written)
>> so what is the logic in tht program..??
>> 2] and i have a initial .gro file and thn i want to insert more number of
>> molecules of tht to a box created i give the command
>> gmx insert-molecules -f .box.gro -ci ab.gro -nmol x -o abc.gro
>> so in the above command the molecules tht i want to insert gets inserted
>> in the empty spaces of the box...How is this defined in the program (such
>> tht the molecules should be inserted into the empty spaces only)..??
>> 3] Yes,I want create an automatic tool in Python which sets up calculations
>> for me  and possibly runs them...
>> So that this Python script calls pdb2gmx, editconf, etc..
>>
>> Thank you
>>
>>
>>   <https://mailtrack.io/> Sent with Mailtrack
>> <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dilip@nitk.edu.in&idSignature=22>
>> <#m_-6789244521733948564_m_6373284441246192622_>
>>
>> On Thu, Apr 27, 2017 at 10:41 PM, Dawid das <addiw7 at googlemail.com>
>> wrote:
>>
>>> Hello Dilip,
>>>
>>>  I don't really get what your problem is. What do you actually want to
>>> do?
>>> Read-in and parse a *.gro file which
>>> is output from MD simulation? Then for instance, your Python script
>>> should
>>> calculate something from, e.g. distance
>>> between centres of masses of residues of interest?
>>> Or do you want create an automatic tool in Python which sets up
>>> calculations for you and possibly runs them?
>>> So that this Python script calls pdb2gmx, editconf, etc.
>>>
>>> I have written various scripts for parsing output files from Gromacs
>>> simulations for my pretty specific purposes.
>>> Anyway if you may find them useful, I will be happy to share them with
>>> you.
>>>
>>> Best wishes,
>>> Dawid
>>>
>>> 2017-04-27 18:53 GMT+02:00 Oliver Beckstein <obeckste at asu.edu>:
>>>
>>> > Hi Dilip,
>>> >
>>> > I think the next version of Gromacs will have some Python bindings.
>>> >
>>> > Until then you can use MDAnalysis http://mdanalysis.org : It reads GRO
>>> > files (as well as XTC, TRR, and TPR, … and many other formats) and
>>> loads it
>>> > into a numpy array.
>>> >
>>> > (If you have questions regarding MDAnalysis please ask on the
>>> MDAnanlysis
>>> > user mailing http://users.mdanalysis.org list instead of the Gromacs
>>> > list.)
>>> >
>>> > Best wishes,
>>> > Oliver (disclosure: I am one of the core developers of MDAnalysis)
>>> >
>>> > > On 27 Apr, 2017, at 09:46, Dilip H N <cy16f01.dilip at nitk.edu.in>
>>> wrote:
>>> > >
>>> > > Hello,
>>> > >
>>> > > I want to write a python program to read a .gro file in gromacs.. How
>>> > can i
>>> > > write the program / code to read the .gro file...
>>> > >
>>> > > I need to write a python programm to read the .gro file and write as
>>> it
>>> > > is.. can anybody help me regarding this...
>>> > >
>>> > > Thank you..
>>> > >
>>> > > --
>>> > > With Best Regards,
>>> > >
>>> > > DILIP.H.N
>>> > > Ph.D Student
>>> > >
>>> >
>>> > --
>>> > Oliver Beckstein, DPhil * oliver.beckstein at asu.edu
>>> > http://becksteinlab.physics.asu.edu/
>>> >
>>> > Assistant Professor of Physics
>>> > Arizona State University
>>> > Center for Biological Physics and Department of Physics
>>> > Tempe, AZ 85287-1504
>>> > USA
>>> >
>>> > Office: PSF 348
>>> > Phone: +1 (480) 727-9765
>>> > FAX: +1 (480) 965-4669
>>> >
>>> > Department of Physics: https://physics.asu.edu/conten
>>> t/oliver-beckstein
>>> > Center for Biological Physics: https://cbp.asu.edu/content/
>>> > oliver-beckstein
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> > --
>>> > 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.
>>> >
>>> --
>>> 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.
>>>
>>
>>
>>
>> --
>> With Best Regards,
>>
>> DILIP.H.N
>> Ph.D Student
>>
>
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>



-- 
With Best Regards,

DILIP.H.N
Ph.D Student