[gmx-developers] Accelerated MD

[Ran Friedman]

Hi,
Are you familiar with the flooding method of Grubmuller? It has been
implemented in Gromacs and seems to be somewhat similar to the algorithm
you describe.
Ran

Gleb Solomentsev wrote:
> Hello Developers,
>
> I am looking into implementing the Hamelberg Accelerated Molecular
> Dynamics (J. Chem. Phys. *120*, 11919 (2004)) algorithm intro the
> latest distribution of gromacs. Basically the algorithm modifies the
> potential function, if the system energy is bellow a certain value. A
> boost energy is applied to help the system escape energy wells when
> bellow an energy threshold. When the system is above the threshold,
> the energies are evaluated according to the original potential.
>
> I am not sure about the best way to structure the modification so
> looking for suggestions. I have been fishing around the development
> list, but not really seeing what I have in mind. Basically, I am
> trying to find where the potential is evaluated for an interaction pair?
>
> Thanks for the help,
> Gleb
>
>
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-- 
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Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355559
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman
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