Did you check if this is possible or not in Plumed
(
http://www.plumed.org/)? Plumed can be interfaced with Amber . ...
Another option that comes to my mind is Colvars module of NAMD/VMD
(
http://colvars.github.io/) .....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 ....
Best
Vlad
On 11/07/2016 02:48 PM, David A Case wrote:
> On Fri, Nov 04, 2016, diego.soler.uam.es 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]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
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Received on Mon Nov 07 2016 - 06:30:02 PST
