Re: [gmx-users] RDF of solvation shell molecules
On 5/23/14, 12:37 AM, sujithkakkat . wrote: Hello Chandan, Thank you for the response. I have used g_rdf, but I guess it gives the RDF for the whole system. Say, if I choose water oxygen, it will plot RDF from water molecules in the whole system. But, I want the RDF for the solvation shell water molecules ,leaving the bulk water . I came across such a plot in an article where the author studied the structure of solvation shell . So do you think it is possible to do that GROMACS? You already have it. The first solvation shell is the first peak in the RDF. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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.
[gmx-users] RDF of solvation shell molecules
Hello, I would like to know if it is possible to plot the RDF of water molecules belonging to the solvation shell of a solute. I mean, I want to know the effect of the solute on the water arrangement in the solvation shell. Is there a way to do this? Regards, Sujith. -- 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.
Re: [gmx-users] RDF of solvation shell molecules
Hi Sujith, g_rdf is the tool you need. Chandan On Thu, May 22, 2014 at 8:18 PM, sujithkakkat . sujithk...@gmail.comwrote: Hello, I would like to know if it is possible to plot the RDF of water molecules belonging to the solvation shell of a solute. I mean, I want to know the effect of the solute on the water arrangement in the solvation shell. Is there a way to do this? Regards, Sujith. -- 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. -- -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India -- 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.
Re: [gmx-users] RDF of solvation shell molecules
Hello Chandan, Thank you for the response. I have used g_rdf, but I guess it gives the RDF for the whole system. Say, if I choose water oxygen, it will plot RDF from water molecules in the whole system. But, I want the RDF for the solvation shell water molecules ,leaving the bulk water . I came across such a plot in an article where the author studied the structure of solvation shell . So do you think it is possible to do that GROMACS? Regards, Sujith. On Thu, May 22, 2014 at 9:31 PM, Chandan Choudhury iitd...@gmail.comwrote: Hi Sujith, g_rdf is the tool you need. Chandan On Thu, May 22, 2014 at 8:18 PM, sujithkakkat . sujithk...@gmail.com wrote: Hello, I would like to know if it is possible to plot the RDF of water molecules belonging to the solvation shell of a solute. I mean, I want to know the effect of the solute on the water arrangement in the solvation shell. Is there a way to do this? Regards, Sujith. -- 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. -- -- Chandan Kumar Choudhury National Chemical Laboratory, Pune India -- 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. -- 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.
