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

[rama david]

Hi justin,
Thank you for help


With Best wishes and Regards,
Rama david


On Wed, Nov 28, 2012 at 7:09 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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<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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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