Re: Can large number of atoms define in colvariables reduce the computational speed in adaptive biased force (ABF) simulation via lowering the GPU utility?

From: Giacomo Fiorin (
Date: Wed Apr 26 2017 - 13:34:12 CDT

Hi Yeping, if the purpose is to define the centers of mass of two protein
domains, you don't really need to include all the atoms. You can check for
yourself that those centers (and the distance between them) don't change
much if you select 1 out of 10 atoms, or e.g. the C-alphas.

Also, the Colvars version bundled with 2.12 includes several optimizations,
including parallelized calculation of centers of mass.

Lastly, it is very hard to understand what you mean by "GPU utility". All
I can say is that the Colvars code runs entirely on the CPU, so it can
benefit from GPU usage only indirectly. Out of all the features of NAMD,
only the most widely used are ported to the GPU.


On Wed, Apr 26, 2017 at 1:51 PM, sunyeping <> wrote:

> Dear all,
> I am trying to do ABF simulation on a protein with a workstation with two
> c2050 GPU. The colvariable I choose is distance. If the distance is the
> distance between two atoms (group1 and group2 both contain one atom), the
> computational speed seems to be normal (about 0.3 day/ns). However, if the
> distance I define is that between the centers of mass (COM) of two protein
> subunits (group1 and group2 both contain about 6000 atoms, the
> computational speed becomes very low (2 day/ns). When I check the GPU
> ultility, I find the two atom distance simulation has a relatively higher
> GPU utility (60%), but the two subunit COM distance simulation has a very
> low GPU utility (4%).
> How can the atom numbers defined in the distance colvariables affact
> the GPU utility? Is there any method to improve this GPU utility and
> computational speed in the COM distance ABF simulation?
> Yeping Sun
> Best regards.

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

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