lloyd.riggs at gmx.ch
Tue Jun 5 16:51:59 CEST 2012
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.
-------- 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
> > 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,
> principle, each frame can have a different number of atoms based on which
> molecules satisfy the given criteria. Each index group that g_select
> 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
> file would work, but I believe that .xtc and .trr files have to have the
> number of atoms in each frame to be interpreted correctly.
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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