rankinb at purdue.edu
Tue Jun 5 18:15:11 CEST 2012
Thank you all for your replies.
Stephan -- can you explain a little more about your 5 line bash script idea? The only part I am not sure about is pulling out the water molecules within a certain distance. Are you suggesting to write a script that calculates atom distance and saves only those within a defined distance?
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of lloyd riggs
Sent: Tuesday, June 05, 2012 10:52 AM
To: jalemkul at vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] Trajectories
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, 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 A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
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