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

Justin Lemkul jalemkul at vt.edu
Wed Nov 28 14:39:27 CET 2012

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 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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