Please keep the discussion on the gmx-users mailing list.
On 1/22/16 3:42 AM, Marta Wisniewska wrote:
Hello Justin, thank you for your response. I know about that way. I'd like to calculate it on piece of paper. I'va already tried do this. But I have small problem and the solutions is not in agreement with data from topolgy file. How can I calculate this?
I don't understand what the question is. How many ions were added? What data do you think are in disagreement? genion really does a very simple operation, so it should be quite obvious what happened. The calculation is nothing more than simple arithmetic.
-Justin
Thank you in advance, Marta Date: Thu, 21 Jan 2016 12:30:36 -0500 From: Justin Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>> To: gmx-us...@gromacs.org <mailto:gmx-us...@gromacs.org> Subject: Re: [gmx-users] trivial question about water molecules Message-ID: <56a115bc.9020...@vt.edu <mailto:56a115bc.9020...@vt.edu>> Content-Type: text/plain; charset=windows-1252; format=flowed On 1/21/16 11:47 AM, Marta Wisniewska wrote: > Hello Gromacs Users; > > I'd like to calculate the # of replaced water molecules by sodium chloride > in my system . I added a 0.15M concentration of NaCl. How can I calculate > the number of water molecules, which are replaced by ions? > genion replaces a water molecule with an ion, so the number of waters replaced equals the number of ions added. -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.
