Nidhi Katyal wrote:
Thank you for your reply.I was able to create isodensity surface but can i color my protein surface according to the difference in flexibility of the backbone caused by addition of some molecule and also know addition of which molecules.Please help.


There are various coloring options in all the visualization programs. Consult the documentation for those; this is not a Gromacs problem and thus if you have difficulty, your best course of action is to ask for help in the appropriate forum.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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