Yes. That is the way to go about it. I was hoping for a more lazy approach... Thanks anyways.
On Tue, Sep 17, 2013 at 5:07 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/17/13 4:50 PM, HANNIBAL LECTER wrote: > >> Is there a smart way of writing the constraint sections in the topology >> file other than entering the values manually ? >> >> > Write a script that parses the [bonds] directive of the post-processed > topology (output by grompp -pp) and write the relevant fields to a > [constraints] directive. > > -Justin > > > >> 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 <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> >>>> < >>>> >>> 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<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> >>>> < >>>> >>> 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<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> >>> >>> > -- > ==============================**==================== > > > 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
