[gmx-users] delete molecule with command line?

Justin Lemkul jalemkul at vt.edu
Wed Aug 20 19:17:13 CEST 2014

On 8/20/14, 5:27 AM, Albert wrote:
> Hello:
> I am just wondering is it possible to delet water molecules within 4A of a
> ligand  through Gromacs command line? Everytime I have to do this in VMD which
> is a little bit complecated.....

g_select can do this.  It can give you an index group of atoms that can be 
passed to trjconv for coordinate extraction.



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

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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