the smart way is to constrain everything at once in MDP... Dr. Vitaly V. Chaban
On Tue, Sep 17, 2013 at 10:50 PM, HANNIBAL LECTER <hanniballecte...@gmail.com> wrote: > 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 -- 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
