[gmx-users] Get some specific frames of traj

Shima Arasteh shima_arasteh2001 at yahoo.com
Mon Jul 8 13:50:30 CEST 2013

Thanks for your earlier suggestions.
I used the command 
g_select -s npt_6.gro -f md_0_1.trr -select 'resname SOL and within 0.1 of (36.0, 36.0, 63.0)' -seltype res_com -selrpos res_com -os
to find water molecule around a specified coordinate. But I  get this error:
Input error or input inconsistency:
selection(s) could not be parsed

Would you please help me with this command? I have not yet tried g_select command.

Thanks in advance.


From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Sunday, July 7, 2013 9:45 PM
Subject: Re: [gmx-users] Get some specific frames of traj

On 7/7/13 1:14 PM, Shima Arasteh wrote:
> Dear gmx users,
> I have a 10 ns simulation trajectory, and like to get some particular frames of it. In fact I want to find the frames in which a specified coordinate is filled with a water molecule, and then pick that frame as an initial structure for the next steps.
> Is there any script implemented in GROMACS tools or any advantageous tool in this approach?

g_select to find the frames of interest, then trjconv -dump to write them out.



Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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