[gmx-users] which file to use to analyze trajectory using code

[Oliver Stueker]

​Hello Sahithya,

the xdrfile library is only one of many ways to write your own code
trajectory analysis.

Other options are:

   - Use  share/gromacs/template/template.cpp ( template.c for Gromacs
   before 5.0) to write your own analysis tool in C++ (or C).
   - Use one of the following Python packages to write your analysis tool
   in Python:
      - pmx (formerly pymacs) https://code.google.com/p/pmx/
      - MDAnalysis  http://www.mdanalysis.org/
      - MDTraj http://mdtraj.org/latest/
   - I believe one can also write plugins for VMD (in tcl or python)

Cheers,
Oliver

On Tue, Jun 9, 2015 at 3:33 AM, Sahithya S Iyer <sah2714 at gmail.com> wrote:

> Thanks for the link Eric !
>
> I am unable to open the following link though -
> ftp://ftp.gromacs.org/pub/contrib/xdrfile-1.1.4.tar.gz
>
>
>
> On Tue, Jun 9, 2015 at 9:31 AM, Eric Smoll <ericsmoll at gmail.com> wrote:
>
> >
> ​​
> Hello Sahithya,
> >
> > Here is one solution:
> > http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library
> >
> > Best,
> > Eric
> >
> > On Mon, Jun 8, 2015 at 9:56 PM, Sahithya S Iyer <sah2714 at gmail.com>
> wrote:
> >
> > > Dear users,
> > >
> > > If one wanted to analyze the trajectory obtained on production run for
> a
> > > property of the protein that is not already defined in the gromacs
> > > programs, which file should be used for analysis ?
> > >
> > > If one were to write an external code to analyze this property, .trr,
> > .tpr,
> > > .xtc files cannot be used as they are binary files. How then can the
> > > trajectory be analyzed ?
> > >
> > > ​Thanks for your time​
> > > --
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> --
> Sahithya S Iyer
> --
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