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

From: Feng Pan <>
Date: Mon, 7 Nov 2016 14:44:10 -0500

Hi, Diego Soler Polo

What you described can be realized in the new NFE (Non equilibrium Free
energy ) module in Amber16.

Basically you need to include the &abmd namelist and set the mode to
UMBRELLA, and set the bias potential file.
The module uses a binary file to store the bias potential, so you need to
convert the ASCII data file to the binary file for input, but this is
should be easy to do.

you are read this updated manual for the details of this method

you can give it a try on the conversion first, if you find any trouble you
can send me the bias potential and I can help you. In the future, I may add
the conversion to AmberTools so this is can be easily done.

Furthermore, you can add a high-dimensional bias potential more than just
one reaction coordinate by this method.

Feng Pan

On Fri, Nov 4, 2016 at 6:02 AM, <> wrote:

> Hi,
> 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.
> Thanks,
> Diego Soler Polo, PhD student
> Universidad Autónoma de Madrid
> _______________________________________________
> AMBER mailing list

Feng Pan
Ph.D. Candidate
North Carolina State University
Department of Physics
AMBER mailing list
Received on Mon Nov 07 2016 - 12:00:02 PST
Custom Search