[gmx-users] aMD for Gromacs?

[Michael Shirts]

Accelerated MD does not give correct dynamics either.  Systems are not
trapped in minima the appropriate amount of time; you can't directly
map the faster movement through space back to the movement in the
original space unless the cutoff energy is so low as to not really
provide any advantage.

I would say that both "metadynamics" and "accelerated MD" are not
necessarily the most precise of names for methods out there . . .

On Tue, Feb 25, 2014 at 8:28 PM, Francis Jing <francijing at gmail.com> wrote:
> 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
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