[AMBER] Replica exchange umbrella sampling

From: Fabrício Bracht <fabracht1.gmail.com>
Date: Fri, 4 Oct 2013 04:00:52 -0300

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?
Thank you in advance
AMBER mailing list
Received on Fri Oct 04 2013 - 00:30:03 PDT
Custom Search