[gmx-users] g_spatial

Justin Lemkul jalemkul at vt.edu
Thu Dec 4 13:55:21 CET 2014

On 12/4/14 3:47 AM, pratibha kapoor wrote:
> Hi,
> I would like to calculate spatial distribution function of my cosolvent
> molecules around peptides. I am using g_spatial tool. I have removed
> periodicity, rotational and translational motion of my solute as suggested
> in the manual. grid.cube file was generated after using g_spatial command.
> But when I set isosurface under the drawing method in vmd, I could see
> nothing. How to visualise it?

Choose an appropriate isovalue in the VMD window?  It usually defaults to zero, 
which is not useful.



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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