[gmx-users] Get some specific frames of traj

Shima Arasteh shima_arasteh2001 at yahoo.com
Tue Jul 9 13:14:31 CEST 2013

I tried the tpr file for -s, but doesn't make difference. 

g_select -s npt_6.gro -f md_0_1.trr -select 'resname SOL and within 0.01 
of (3.6, 3.6, 6.3)' -seltype res_com -selrpos res_com -os

Would you please give me suggestions? I found some resemble commands in mailing list but didn't find the problem with my command.

Thanks in advance.


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Monday, July 8, 2013 9:14 PM
Subject: Re: [gmx-users] Get some specific frames of traj

On 7/8/13 7:50 AM, Shima Arasteh wrote:
> 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.

g_select -select 'help all' provides a huge amount of information.  Have you 
tried passing a .tpr file to -s instead?  Are your units right?  It would seem 
your box is very big.



Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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