[gmx-users] Free Energy calculation

[Justin Lemkul]

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 <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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-- 
==================================================

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

==================================================