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 -- ================================================== 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
