On 11/18/14 11:46 PM, RINU KHATTRI wrote:
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
You can calculate diffusion coefficients with g_msd.
-Justin
On Fri, Nov 14, 2014 at 12:04 AM, Justin Lemkul <jalem...@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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