Thanks for the reply Justin. I have tried the following: g_select -f prodrun.xtc -s prodrun.tpr -n index.ndx -os size.xvg - oc cfrac.xvg -oi index.dat -select '"Nearby water" resname SOL and within 0.35 of group Protein'
But there is a syntax error. Could you please tell me where i could be going wrong.. On Tue, Jun 9, 2015 at 5:12 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > 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. > -- Sahithya S Iyer -- 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.