[gmx-users] Clarification for the meaning of ncoords in GROMACS 5.0.4 pull code

Justin Lemkul jalemkul at vt.edu
Sun Mar 26 16:16:30 CEST 2017

On 3/24/17 1:54 PM, Sajeewa Pemasinghe wrote:
> Hi,
> I have two molecules which are not moving in the z axis due to being
> continuous across the periodic boxes. I want to keep the distance between
> them fixed by pulling along x and y axes. So as I am pulling along x and y
> axes does my ncoords = 2 ?  By going along with this logic as long as my
> pull-geometry = distance, will the maximum number for ncoords be 3 (i.e.
> pulling along all x, y , and z axes)? I really appreciate an explanation.

The "pull-ncoords" option tells grompp how many biasing potentials there are, 
not anything to do with which Cartesian directions are biased.



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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