[gmx-developers] Accelerated MD

Alexander Herz aherz.kazan at arcor.de
Tue Oct 27 13:22:09 CET 2009


for a first quick overview of mdrun you might look here:


Gleb Solomentsev schrieb:
> 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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