[gmx-users] creating index for first hydration layer water molecules

[Justin Lemkul]

On 6/9/15 5:11 AM, Sahithya S Iyer wrote:
> Dear Users,
>
> The first hydration layer, to the best of my understanding, is the first
> minimum in the protein (backbone)-water radial distribution function. How
> do I create an index for the water molecules in the first hydration layer?
>

The hydration layer around a protein includes the full protein, not just the 
backbone.  You can, of course, analyze whatever makes sense to you, but the 
whole protein is typically considered in most experiments, and certainly is the 
case if anyone talks about the "protein hydration layer."

gmx select can do this.  See examples in the help info.

-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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