[gmx-users] Trajectories

[lloyd riggs]

Dear Rankinib,

You can do it with a 5 line bash script as well, cat everything times x,y,z and just cut and past them into a spread sheet, and save it with tabs or spaces.

Stephan Watkins

-------- Original-Nachricht --------
> Datum: Tue, 05 Jun 2012 09:05:09 -0400
> Von: "Justin A. Lemkul" <jalemkul at vt.edu>
> An: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Betreff: Re: [gmx-users] Trajectories

> 
> 
> On 6/5/12 9:02 AM, rankinb wrote:
> > I am interested in pulling out the trajectories (x,y,z coordinates) of
> water
> > molecules within a certain distance of my solute molecule.  I have tried
> > using g_select, but that will only give me the atom numbers and not the
> > trajectories.  I can create an index file using this command but
> > unfortunately each time frame is set as a different group.
> >
> > Is there a way to get the trajectories at all frames of only the water
> > molecules within a specified distance of a solute molecule?
> >
> 
> At present, there is no elegant way to construct such a trajectory, since,
> in 
> principle, each frame can have a different number of atoms based on which
> water 
> molecules satisfy the given criteria.  Each index group that g_select
> provides 
> corresponds to an individual frame in the original trajectory, which you
> can use 
> to pull out individual coordinate files.  Perhaps a multi-frame .pdb or
> .gro 
> file would work, but I believe that .xtc and .trr files have to have the
> same 
> number of atoms in each frame to be interpreted correctly.
> 
> -Justin
> 
> -- 
> ========================================
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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