Re: [AMBER] Replica exchange umbrella sampling

From: Jason Swails <>
Date: Fri, 4 Oct 2013 07:17:12 -0400

On Fri, Oct 4, 2013 at 3:00 AM, Fabrício Bracht <> wrote:

> Hi all. Would it be possible to obtain the minimum free energy path of a
> mechanism similar to the Grotthuss mechanism using umbrella sampling with
> replica exchange. Let me try to contextualize this a bit more. For
> instance, by stating that a proton exchange between three molecules (say
> one hydronium and two water molecules) occurs in a concerted manner, that
> does not mean that the distances between the exchanging protons relative to
> their accepting oxygen atoms are the same. This depends a lot on the
> surroundings, temperature...etc. So by simply using LCOD, for example,
> between the exchanging pairs to describe these transfers, one would have to
> try every combination (within reasonable known distances between pairs) in
> order to obtain the path with the lower energy. Since I cannot use the
> excess of charge coordinate to perform this type of simulation in amber,
> nor can I use plumed (and its fancy variables customization properties)
> with amber12, I thought that REMD might be a solution.
> Does this sound like a reasonable proposal?

You can look at the adaptively biased MD options, which provide many
similar collective variables as plumed. But as far as REMD is concerned --
what type of REMD do you propose? T-REMD? Umbrella sampling-REMD? You
can certainly use it, but I don't see how REMD solves any of the problems
you have described. With T-REMD, I don't think you can see rapid proton
diffusion at reasonable temperatures, whereas with umbrella sampling-REMD
you still need to define your reaction coordinate the same way you would
without replica exchange. Based on your statement about using LCOD, I take
it that this approach is somewhat intractable.

(Whatever you choose, though, requires using a flexible water model and
turning off SHAKE, I would imagine, which further reduces the time step you
can use).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Oct 04 2013 - 04:30:05 PDT
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