[gmx-users] About the biotin parameter.....

[Justin Lemkul]

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

-- 
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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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