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

[Gaurav Goel]

VMD allows you to color code the trajectory based on the frame number-
exactly what you want to do.

-g

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
>> 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
>
> --
> ==================================================
>
> 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
> http://mackerell.umaryland.edu/~jalemkul
>
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>
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-- 
Gaurav Goel, PhD
Assistant Professor
Department of Chemical Engineering
Indian Institute of Technology, Delhi
Hauz Khas, New Delhi 110016
India