[gmx-users] Accelerated MD in GROMACS

[Mark Abraham]

Hi,

Absolutely. It's merely a question of prioritising limited resources. For
example, one has to be able to answer "why should one use aMD rather than
AWH?" in order to consider implementing a new method. Then it has to impact
a bunch of people, or be immediately useful to the developer / their
colleagues, in order for someone to choose to pay for the work.

Mark

On Tue, Jul 5, 2016 at 3:29 PM James Starlight <jmsstarlight at gmail.com>
wrote:

> Hello Mark,
>
> probably to implement of aMD in Gromacs will be very good as well:  it
> will allow to use this protocol with the CG martini systems - where to
> accelerate sampling of diffusion using double boost approach of amd
> seems very attractive option for modeling of protein-protein binding
> for instance. Compared to others MD packages - combining of those
> points  will be only available for GROMACS users ;-)
>
> James
>
> 2016-07-05 13:00 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:
> > Hi,
> >
> > In general, one should look at the release notes of software to see what
> > new features were added in a version. This will tend to be findable with
> > Google also :-)
> >
> > Accelerated MD has never been implemented to my knowledge. It would
> > probably be fairly easy, but so far nobody with a suitable problem has
> > wanted to write the code. Alternatively, AWH
> > http://scitation.aip.org/content/aip/journal/jcp/141/4/10.1063/1.4890371
> is
> > implemented, and will likely be available shortly for people to use,
> based
> > on the upcoming GROMACS 2016, but won't be formally part of the 2016
> > GROMACS release.
> >
> > Mark
> >
> > On Tue, Jul 5, 2016 at 12:47 PM James Starlight <jmsstarlight at gmail.com>
> > wrote:
> >
> >> Dear Gromacs users!
> >>
> >> I wonder t ask whether the aMD was implemented within GMX-5 ?  I am
> >> looking for the non-equilibrium md protocol with the possibilities to
> >> apply one or two boosts on the system to accelerate some diffusion
> >> events within it.
> >>
> >> Thanks !
> >>
> >> James
> >> --
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