[gmx-users] Doubt about gmx wham analysis

[Justin Lemkul]

On 6/2/17 7:20 AM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
> 
> I would like to correct myself. Actually, the COM of the two groups - Protein and Ligand are about 5 nm away at the end of the pulling process. But the rear end of the ligand is just 0.6 nm away from the closest Amino acid of the Protein. Is that reasonable for the Binding affinity calculations?
> 

0.6 nm is certainly well within the short-range nonbonded cutoffs, so no, you 
have not achieved a reasonably dissociated state.

-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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