[gmx-users] Insert molecules in system with minimum distance between them

Justin Lemkul 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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