[gmx-users] color-coding molecule location at different time frame

Justin Lemkul jalemkul at vt.edu
Wed Mar 23 01:13:10 CET 2016

On 3/22/16 12:39 PM, Jagannath Mondal wrote:
> Dear gromacs-users
>    I have a system of protein-ligand system.  I would like to use different
> color for ligand location at different time-frame. The final goal is to
> have a snapshot where ligand location of all time frame are color-coded
> using a color-gradient ( for example : red at short time and blue at long
> time). How can I achieve that ?

Most, if not all, visualization programs allow you to color by occupancy or 
B-factor in a PDB file.  So simply come up with some scale of values that 
indicates progress through the simulation and write those values in the 
appropriate field.  None of that really has to do with GROMACS, though, as it's 
all external scripting and visualization.



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