[gmx-users] Adding polyatomic ions using genion or genbox ..
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
More information about the gromacs.org_gmx-users