[AMBER] Umbrella simulation with an arbitrary bias potential

From: <diego.soler.uam.es>
Date: Fri, 04 Nov 2016 11:02:04 +0100


  I would like to perform simulation with arbitrary bias potentials of
my choice. Let's say I have a particular reaction coordinate, Y, and
that I have a potential energy function V(Y) which I want to use as
bias potential.

In practice, this bias potential would be described in a file
"bias_pot.dat" whose format would be as follows: N+1 columns, with N
the dimensionality of the reaction coordinate Y; N first columns
specifying values of the reaction coordinate along a certain grid with
which I discretize the possible values of Y; and the (N+1)th column to
specify the values of V(Y) in each row.

Next, I would like to perform a MD simulation with the bias potential
specified in my file "bias_pot.dat". The idea would be that, at each
step of the MD simulation, the program would check the value of the
reaction coordinate, Y, and compute V by interpolation over the rows
of the file "bias_pot.dat"

Is this possible in AMBER? I don't know if it is, but it would
certainly be great, because it would add a great deal of flexibility
for Umbrella simulations.


Diego Soler Polo, PhD student
Universidad Autónoma de Madrid

AMBER mailing list
Received on Fri Nov 04 2016 - 03:30:02 PDT
Custom Search