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

[Dilip H N]

and how are the x,y,z coordinates, velocities assigned with the values..??
the logic behind them in gromacs

Thank you



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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
>
>
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> <#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/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
>



-- 
With Best Regards,

DILIP.H.N
Ph.D Student