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

[Dawid das]

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
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> Center for Biological Physics: https://cbp.asu.edu/content/
> oliver-beckstein
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