Hi Justin, I just want to ask how is the r(nm) in posre.itp working?
I would like to put semi-permeable wall on +/- 2.4 nm in z coordinate of the box. When I write 2.4 in the r(nm) property for [position_restraints] in posre.itp, it seems all of the molecules that I apply flat-bottom restraint travel +/- 2.4 nm. But I do not want this, I would like to put a wall or force on +/-2.4 nm in z of the box. Do you have any advice about this? Thanks in advance. > On 21 Mar 2016, at 18:37, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 3/21/16 1:29 PM, gozde ergin wrote: >> Ok this was a silly question. >> In g_energy command 5. one is flat-bottom posres force. >> Sorry. >> > > The output of g_energy is energy, not force. > > But the quantity is simple to calculate. If you have applied a flat-bottom > restraint along z, then you just need the time series of the z-coordinates of > the restrained particles. > > F = k*(z-z0), where z0 is the position at which the flat-bottom restraint is > active. Since there are two walls, then you need to conditions, for +/- z0 > and then the final sum should be divided by 2 before being divided by the > area of the semipermeable wall. > > -Justin > >>> 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. >>> >> > > -- > ================================================== > > 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 <mailto:jalem...@outerbanks.umaryland.edu> > | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > <http://mackerell.umaryland.edu/~jalemkul> > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List > <http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List> before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > <http://www.gromacs.org/Support/Mailing_Lists> > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> or send > a mail to gmx-users-requ...@gromacs.org > <mailto: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.
