[gmx-users] mdp

[Mark Abraham]

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
> >
> > ==================================================
> >
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