[gmx-users] Free Energy calculation

[RINU KHATTRI]

Thank you justin is there any tutorial like kalp in dppc which i can follow
how can i calculate the diffusion coefficient of ligand(drug)
thanks in advance

On Fri, Nov 14, 2014 at 12:04 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 11/13/14 4:09 AM, RINU KHATTRI wrote:
>>
>> hello gromacs users i am working on protein ligand complex with popc
>> membrane i want to calculate the free energy of protein and ligand i
>> have to follow which tutorial (methane in  water) but my protein is
>> membrane protein i am also running md simulation (70 ns)  i am new in
>> free energy calculation from where i have to start after the
>> production md or  i can start from the original pdb file
>
>
> The "free energy of protein and ligand" is a rather ill-defined quantity.
> Are you trying to calculate binding free energy?  If so, there's a huge
> amount of literature on this topic.  It comes down to simply doing a
> thermodynamic cycle of the ligand in water and in the binding site.
> Restraints might be needed to keep the ligand bound while being decoupled,
> but again there's tons of papers on this topic.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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