[gmx-users] (no subject)

[Justin Lemkul]

On 11/17/14 9:15 AM, behnaz abdolmaleki wrote:
> Dear all
>
> I want to calculate free energy by g_lie, but I do not know how to select
> the length of  box for free ligand simulation.should I select the dimension
> of box for ligand simulation (in free situation ) as same as the dimension
> of box in complex simulation (receptor-ligand)? or I can do whit another
> lenght ?
>

The box just needs to be large enough to avoid minimum image violations, like 
any other simulation; the goal there is to obtain nonbonded interaction energies 
between the ligand and solvent, so it's not particularly special in its setup.

-Justin

-- 
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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

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