[gmx-users] g_select gromacs version 4.6.3

Justin Lemkul jalemkul at vt.edu
Mon Aug 31 01:36:09 CEST 2015

On 8/30/15 5:40 PM, Stephanie Teich-McGoldrick wrote:
> Hello all,
> I am using gromacs version 4.6.3 and am having difficulty with g_select. I
> am trying to create a list of all water molecules in which any atom in the
> molecule has a z position less than 2nm. However, my list has partial
> molecules in it. My command is as follows:
> g_select -f traj.trr -s topol.tpr -select 'resname SOL and res_com z < 2.0'
> -on L1_index_select_0.ndx -b 0 -e 0 -rmpbc
> I think that I need to specify 'resname SOL and  same molecule and res_com
> z< 2.0', however, this syntax does not work.

Try something like

same residue as resname SOL and z < 2.0



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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