[gmx-developers] Accelerated MD

Ran Friedman r.friedman at bioc.uzh.ch
Tue Oct 27 12:35:04 CET 2009

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.

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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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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