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

[Sahithya S Iyer]

Thanks Oliver !

On Tue, Jun 9, 2015 at 7:24 PM, Oliver Stueker <ostueker at gmail.com> wrote:

> ​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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-- 
Sahithya S Iyer