Yes it worked. I appreciated to your help Justin. Thanks a lot. > On 07 Apr 2016, at 21:37, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 4/7/16 12:57 PM, gozde ergin wrote: >> 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. > > This is expected. The flat-bottom potential is established with respect to > the reference coordinates. > >> 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? >> > > If you want walls at given z-values, the z-coordinate of species to which the > restraint is applied have to be set to zero. This coordinate file is passed > to grompp -r as the reference point for the potential. > > -Justin > >> 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> >>> <mailto:jalem...@outerbanks.umaryland.edu >>> <mailto:jalem...@outerbanks.umaryland.edu>> | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> <http://mackerell.umaryland.edu/~jalemkul> >>> <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><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> >>> <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> >>> <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> >>> <mailto:gmx-users-requ...@gromacs.org >>> <mailto: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 | (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.
