[gmx-users] mdp

[Mouri Ahmed]

Thanks Mark

I will check the force field.

Best Regards
Mouri




On Tue, Oct 18, 2016 at 3:00 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> What does your background reading on applications of that force field
> suggest to you?
>
> Mark
>
> On Tue, 18 Oct 2016 01:27 Mouri Ahmed <mouriahmedmou at gmail.com> wrote:
>
> > Hi
> >
> > Thanks Justin and Parvez for your suggestions.
> >
> > Can I use "constraints=none" for coarse-grain protein also?
> >
> >
> > Best Regards
> > Mouri
> >
> >
> >
> >
> > On Mon, Oct 17, 2016 at 8:53 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> > >
> > >
> > > On 10/16/16 2:16 PM, Parvez Mh wrote:
> > >
> > >> Hey;
> > >>
> > >> Go through the link <http://manual.gromacs.org/
> online/mdp_opt.html#bond
> > >.
> > >> You will get everything about your purpose. By the way,  you could use
> > >> *constraints=none
> > >> .  *But you have to make sure you use proper *timestep* while using no
> > >> constraint.
> > >>
> > >>
> > > Constraints such as SETTLE for rigid water would also have to be turned
> > > off with "define = -DFLEXIBLE" but most water models are not designed
> to
> > be
> > > used in flexible form, so this is not typically done during MD.
> > >
> > > -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
> > >
> > > jalemkul at 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-request at 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-request at 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-request at gromacs.org.
>