Ok this was a silly question. In g_energy command 5. one is flat-bottom posres force. Sorry.
> On 21 Mar 2016, at 17:26, gozde ergin <gozdeeer...@gmail.com> wrote: > > Hey Justin, > > I am just wondering in order to estimate the osmotic pressure I need extract > the flat-bottom restraint force. (Force/Area = Pressure) > Do you have any idea to how to extract this force? > > Thanks in advance > > > >> On 10 Mar 2016, at 15:58, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >> >> On 3/10/16 4:44 AM, gozde ergin wrote: >>> Dear Justin, >>> >>> Thanks for your respond, I assume there is a way to apply this restraint on >>> specific molecules. >>> Because my system is mixed with organic and water and I would like to apply >>> these forces on organic molecules not water? >>> >> >> So apply flat-bottom restraints to whatever the organic molecules are. It's >> not something specific to ions. You set the restraints in the molecule's >> topology (in its [moleculetype]), construct a reference coordinate file that >> defines some unphysical coordinates to be used as the center of the >> restraint, and that's it. I've described the process in detail before so >> check the archive. >> >> -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. > -- 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.
