On 11/28/12 8:08 AM, rama david wrote:
Hi justin thank you for suggestion.
I think to Calculate the free energy of solvation of biotin, I hve to use
the method
as per your tuotorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html
Is these right or I have to do anything else???
That is the general workflow, though the .mdp settings will need to be modified
and you will need to do both van der Waals and Coulombic transformations. I
would also assume that you will need longer simulations and more lambda points
to define the transformation, since biotin is considerably more complex than
methane.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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