[gmx-users] Format for predefined positions insert-molecules

Justin Lemkul jalemkul at vt.edu
Wed Mar 29 18:55:52 CEST 2017

On 3/29/17 12:52 PM, Svetomir Hitov wrote:
> Hello,
> I have been going through the documentation and mailing list for the last
> couple of days, but I cannot find anywhere, what the format for the
> predefined insertion trial positions should be. Insert-molecules should use

I'd start with the last paragraph of the help information:

"Alternatively, the molecules can be inserted only at positions defined in
positions.dat (-ip). That file should have 3 columns (x,y,z), that give the
displacements compared to the input molecule position (-ci). Hence, if that
file should contain the absolute positions, the molecule must be centered on
(0,0,0) before using gmx insert-molecules (e.g. from gmx editconf -center).
Comments in that file starting with # are ignored."


> that file to place molecules inside the box in certain places. I have tried
> plain text file with several coordinates. Insert-molecules is not giving any
> error but yet it is inserting molecules randomly. I want to make it insert
> molecules just in one half of the box.
> Thank you in advance!


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


More information about the gromacs.org_gmx-users mailing list