[gmx-users] Doubt about Free Energy Calculations using g_bar

[Justin Lemkul]

On 6/8/17 11:46 AM, Varvdekar Bhagyesh Rajendra wrote:
> Dear all,
> 
> I am attempting to find Binding affinity of a Protein-ligand system by following the Free Energy tutorials (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html).
> It says : "The procedure in this tutorial essentially assumes that charges have been properly been turned off prior to this point". How do we turn off the charges of a group specified in an index file (the ligand in my case) ?
> 

Either set them to zero in the topology or define couple-lambda0 = vdw and 
couple-lambda1 = none.

-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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