[gmx-users] Adding polyatomic ions using genion or genbox ..

Justin Lemkul jalemkul at vt.edu
Fri Jun 13 14:38:19 CEST 2014

On 6/13/14, 7:33 AM, Alberto Sergio Garay wrote:
> Dear Users:
> I would like to know if it is possible to add some polyatomic ions inside a
> pre-equilibrated (water + solute) system using genion or genbox...?
> I don't want to lose my equilibrated water around my macromolecule...
> If this is not possible can you give any piece of advice of how I can do it..

In either case (adding before or after solvation), genbox -ci -nmol is the way 
to go.  Depending on the size of your polyatomic ions, they may fit in the 
pre-equilibrated system.  If not, you could (in theory) strip the water from 
your existing system and save it to a coordinate file, then insert your 
polyatomic ions around the macromolecule, then re-solvate with the saved, 
equilibrated water.  But if you're going to re-build it, re-equilibrating is 
trivial anyway, and probably less work.



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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