[gmx-users] color-coding molecule location at different time frame
gauravgoeluta at gmail.com
Wed Mar 23 04:44:32 CET 2016
VMD allows you to color code the trajectory based on the frame number-
exactly what you want to do.
On Wed, Mar 23, 2016 at 5:42 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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
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Gaurav Goel, PhD
Department of Chemical Engineering
Indian Institute of Technology, Delhi
Hauz Khas, New Delhi 110016
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