[AMBER] Defining aMD Boost Parameters (Range and Distribution) for Hamiltonian Replica Exchange

From: Jason Ku Wang <jwang198.stanford.edu>
Date: Mon, 18 Jun 2018 18:09:18 -0700

Hi AMBER Community,

I am interested in running Multidimensional Replica Exchange (2D) using
Hamiltonian and temperature dimensions.

I have a good idea of how the temperature dimension is defined. Based on
previous literature, 310-380K seems to be a good range. Then, to define the
temperature distribution to fit that range, I can use the following
calculator: http://folding.bmc.uu.se/remd/ which takes into account system
size, NPT vs. NVT, and a target exchange probability.

For the Hamiltonian dimension, I am using accelerated Molecular Dynamics
(aMD) applied only to the torsional/dihedral potential energy terms. The
question I am stuck on is: *for a given target exchange probability (e.g.
20%) and protein system, is there an accepted method to define 1) the
range, and 2) the distribution of boost parameters (alphaD and
EthreshD) used to create varying torsional/dihedral boost potentials?*

Based on the aMD AMBER tutorial
<http://ambermd.org/tutorials/advanced/tutorial22/section2.htm>, there
seems to be a suggested value for both alphaD and ethreshD, but how does
one extend this to define a range and distribution of such parameters?

Thanks so much for the help!

Jason Wang
Stanford University, Class of 2018
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Received on Mon Jun 18 2018 - 18:30:01 PDT
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