Re: Colvars alternative recommendations

From: Giacomo Fiorin (
Date: Mon Apr 30 2018 - 09:31:57 CDT

Hi Zack, how large is the number of atoms? Note that the regular radius of
gyration code is not parallel either, although it would be definitely
faster than a custom function via Lepton.

Is the exponent P an even integer? It wouldn't be a big deal to have P as
an option, rather than being hard-coded. It may even be possible to
calculate the inverse gradients for the corresponding expression, and
estimate free-energies through the internal forces (as in straight ABF)
rather than the applied ones (as in eABF or metadynamics).

FYI, PLUMED supports Lepton expressions, as well. Support for it was added
immediately after the corresponding one in Colvars, so it should behave
more or less the same way given that Lepton has a simple API.

If you can define in more detail the NN or GPR methods that you plan on
using, I can recommend whether it's easier to port it into NAMD or switch
to another MD engine.


On Mon, Apr 30, 2018 at 9:57 AM, Zachary Ulissi <> wrote:

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

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD

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