[gmx-users] aMD for Gromacs?

[Francis Jing]

In fact there is one major difference: metadynamics does not have dynamics!
Although a recent version have dealt with it, its implementation may
require some time.
Anyway, it's fine if you do not care about dynamics.

Francis


On Wed, Feb 26, 2014 at 6:39 AM, Michael Shirts <mrshirts at gmail.com> wrote:

> Your best bet is probably something like the PLUMED plugin to do
> metadynamics.  aMD raises up the potential if it is below a given
> cutoff; metadynamics puts in bumps in the potential where you have
> visited.  There are definitely subtle differences, but the general
> effects are similar.
>
> On Tue, Feb 25, 2014 at 1:31 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >
> > On 2/25/14, 1:03 PM, Albert wrote:
> >>
> >> Hello:
> >>
> >> Does anybody knows can we do Accelerated molecular dynamics (aMD,
> >> developed in
> >> Mccammon group) in Gromacs? I seldom
> >> see someone did this in Gromacs....
> >>
> >
> > Gromacs has flooding, which I think is similar.  But as far as aMD, no.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA 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 at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> >
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-- 
Zhifeng (Francis) Jing
Graduate Student in Physical Chemistry
School of Chemistry and Chemical Engineering
Shanghai Jiao Tong University
http://sun.sjtu.edu.cn