[gmx-users] aMD for Gromacs?
mrshirts at gmail.com
Tue Feb 25 23:39:31 CET 2014
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:
>> 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 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
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