[gmx-users] Get some specific frames of traj

Justin Lemkul jalemkul at vt.edu
Mon Jul 8 18:44:19 CEST 2013

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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