MetaDynamics in 2.9b2 Question

From: Aron Broom (
Date: Wed Apr 04 2012 - 14:54:39 CDT

I had two questions concerning metadynamics in NAMD 2.9b2, the first quite
specific to 2.9b2, and the other perhaps is more general and could relate
to 2.8 also.

1) In 2.8 multiple replicas (multiple walkers) metadynamics was not
possible while useGrids was enabled, but I see the particular note
concerning this has been removed from the 2.9b2 user guide. It does,
however, say that a *.hills file is used for each replica as a kind of
communication buffer, which perhaps suggest that the hills still need to be
recorded analytically? Anyway, I'm wondering if it is possible now to do
multiple walkers/replicas for metadynamics while also having the benefit of
the grids.

2) Is it possible (has anyone done this in NAMD?) to use the temperature
replica exchange Tcl script to perform Replica-Exchange metadynamics? I
don't see why it would be different in form from any other
temperature-based replica exchange method, but as I'm no expert in these
things I could easily be missing something. Moreover, the section on
temperature replica exchange claims that the scripts are in spirit easily
adapted for exchange based on things other than temperature. Is it
therefore possible to perform bias-exchange metadynamics? Could one even
combine both of those in order to do nested replica exchange for different
parameters (temperature and bias for instance)?



Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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