Colvars alternative recommendations

From: Zachary Ulissi (
Date: Mon Apr 30 2018 - 08:57:27 CDT

Hi - we're currently doing ABF simulations using NAMD/colvars. We're using
something like a generalized radius of gyration of a group of particles -
same definition, but a power P greater than 2:
R_g = [ \sum (R-R_{COM})^P ] ^(1/P)

1) We currently have this implemented using the lepton custom function code
in the NAMD colvars module, which works well but is not parallel and does
not scale well with # of particles. Does anyone have a suggestion for
improving this? Hand-coding a TCL custom colvar was definitely slower.

2) We're planning to repeat this calculation many times with differences in
structures, so we will have significant prior information about the shape
and smoothness of the final potential. Using something like a gaussian
process/ kriging seems like an obvious way to accelerate the process (and
we can input smoothness ahead of time), but I don't see that implemented in
colvars. The NN code in SSAGES looks interesting but as far as I know does
not support NAMD. PLUMED looks similar but I don't think there is something
like lepton or the generalized radius of gyration above, so I'm a little
hesitant to jump in. Are there other colvar/metadynamics codes I should be



Zachary W. Ulissi
Assistant Professor
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh PA 15213
(412) 268-9517

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