Is there a smart way of writing the constraint sections in the topology file other than entering the values manually ?
On Tue, Sep 17, 2013 at 10:10 AM, rahul seth <rahul.seth.grom...@gmail.com>wrote: > Thanks > > > On Tue, Sep 17, 2013 at 10:03 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > On 9/17/13 10:00 AM, HANNIBAL LECTER wrote: > > > >> Is there a way to constraint bonds of a part of the system while keeping > >> the other part flexible? For example for a simulation with two > proteins, I > >> would like to constraint the bonds of one and would like to keep the > other > >> flexible. > >> > >> I would prefer to use LINCS to constraint the system > >> > >> > > Set the constraints explicitly in the topology of one protein using a > > [constraints] directive. Then set "constraints = none" in the .mdp file. > > The constraints read from the topology will override the .mdp setting > > while leaving all other bonds unconstrained. > > > > -Justin > > > > -- > > ==============================**==================== > > > > Justin A. Lemkul, Ph.D. > > 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 > > > > jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> > | (410) > > 706-7441 > > > > ==============================**==================== > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/**mailman/listinfo/gmx-users< > http://lists.gromacs.org/mailman/listinfo/gmx-users> > > * Please search the archive at http://www.gromacs.org/** > > Support/Mailing_Lists/Search< > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting! > > * Please don't post (un)subscribe requests to the list. Use the www > > interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists< > http://www.gromacs.org/Support/Mailing_Lists> > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
