[gmx-users] Trajectories

[Blake Rankin]

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?

Thanks,
Blake  

-----Original Message-----
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

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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