[gmx-users] Insert molecules in system with minimum distance between them
jalemkul at vt.edu
Thu Oct 1 14:22:45 CEST 2015
On 9/30/15 12:15 PM, Ebert Maximilian wrote:
> Dear list,
> I am trying to add n-number of molecules in my prepare protein+water+ions box but keep a minimum distance of 1 nm in all directions between the newly inserted molecules. On top of that I want to replace solvent molecules with the newly added molecules. So basically I am looking for gmx genion with the -rmin flag for non ions.
> Which tool could I use?
No GROMACS tool will do this. You can use gmx insert-molecules in concert with
a positions.dat file (with pre-computed locations for the molecules), followed
by gmx solvate.
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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