[gmx-users] Free Energy calculation
nickname.mittu at gmail.com
Wed Nov 19 05:46:50 CET 2014
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 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
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