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Feature #1634

Boxed Molecular Dynamics

Added by Jonathan J Booth almost 5 years ago.

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New
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Normal
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Description

Boxed Molecular Dynamics is an enhanced sampling method for the simulation of rare events such as protein conformational changes and reactions with a large barrier. IF it could be implemented in Gromacs and work in parallel or on GPU clusters this woudl vastly ncrease the usefulness of the method and enable larger systems and longer timescale processes to be studies.

The method is described here:

http://scitation.aip.org/content/aip/journal/jcp/137/16/10.1063/1.4759088

And some recent application here:
http://rsta.royalsocietypublishing.org/content/372/2021/20130384.full

The method is simple. A reaction coordinate is defined and reflecting boundaries places along it at certain threshold values. If during a trajectory one of these threshold values is reached then the parallel projection of the velocities along the reaction coordinate is inverted. In practice this is easy to implement. Please feel free to contact me if you require any examples of the method or the code.

Thanks

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