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

[Dilip H N]

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


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

DILIP.H.N
Ph.D Student