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

From: Vlad Cojocaru <>
Date: Mon, 7 Nov 2016 15:01:43 +0100

Did you check if this is possible or not in Plumed
( Plumed can be interfaced with Amber . ...
Another option that comes to my mind is Colvars module of NAMD/VMD
( .....But I am not sure whether you can do
exactly what you propose .... If not, perhaps could be easy to implement
in such software already dedicated to order parameters ....


On 11/07/2016 02:48 PM, David A Case wrote:
> 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.
> ...regards...dac
> _______________________________________________
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Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]
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Received on Mon Nov 07 2016 - 06:30:02 PST
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