Re: Colvars alternative recommendations

From: Zachary Ulissi (
Date: Mon Apr 30 2018 - 09:50:35 CDT

Hi - currently we have ~250 atoms in the colvar, though considering just
some portion of each molecule we can push that down. The speed is
especially apparent right now because we're doing implicit solvent, but it
will be a smaller fraction when we do explicit and force call times go up.

Yes, P is an even integer. We are using this as a softer metric for the
size of a group of molecules than the outer limit (containing sphere). We
also define/use this in 1 or 2 dimensions (so radius of gyration in a
plane, or radius of gyration along a line, using the XY or Z components
only, respectively). Yes, adding it as an option would be great!

Thanks for the tip about PLUMED; I'll take a closer look.

Regarding GPR/NN I was thinking something along these lines:

GPR feels more reasonable to me than NN for guarantees, bounded nature,
uncertainty propagation, incorporation of prior information on correlation
structure, etc.


On Mon, Apr 30, 2018 at 10:32 AM Giacomo Fiorin <>

> 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.
> Giacomo
> 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

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

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