[gmx-users] aMD for Gromacs?

Albert mailmd2011 at gmail.com
Wed Feb 26 08:29:32 CET 2014

Thanks a lot for kind comments guys.

recently I found a PNAS paper using aMD to explore the process of GPCR 
activation which take place at minisecond time scale:


it seems that it can sample mini second events, but  cannot assign 
proper sequential time for each frame. Probably this is also a weakness 
of metadynamics? I am just wondering is it possible to figure out the 
sequence of each conformation take place in either methods?



On 02/26/2014 06:02 AM, Michael Shirts wrote:
> 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 . . .

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