[gmx-users] .trr forces into VMD

Berk Hess gmx3 at hotmail.com
Tue May 19 16:55:35 CEST 2009


g_traj can write |f| or components of f in the b-factor field of a pdb file.
I guess VMD can read and display that.
I don't know if that will fulfill your needs.


> Date: Wed, 20 May 2009 00:19:59 +1000
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] .trr forces into VMD
> Matteus Lindgren wrote:
> > Hi all
> > 
> >  
> > 
> > I am looking for a way to import forces from a gromacs run into VMD for 
> > analysis. From a mdrun –rerun I have forces in a .trr file but VMD only 
> > reads the coordinates. Can you think of any way to get the forces into 
> > vmd instead of the coordinates?
> If VMD will only import positions from .trr files, then you could write 
> a forces-only .trr file and through a code hack or hex edit, force the 
> frame header to describe them as positions. Or, write a new VMD plugin. 
> Or, modify the VMD source suitably.
> Mark
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