Re: [AMBER] Umbrella simulation with an arbitrary bias potential

From: David A Case <>
Date: Mon, 7 Nov 2016 08:48:07 -0500

On Fri, Nov 04, 2016, wrote:
> 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"

What you describe is not implemented in Amber. Might be an interesting idea
for someone to pursue.


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Received on Mon Nov 07 2016 - 06:00:05 PST
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