Cost of a colvar calculation

From: George Patargias (
Date: Tue Jul 22 2014 - 06:27:52 CDT


I am comparing the Benchmark times for a given system (~258,000 atoms) using
NAMD_CVS-2014-06-02_Source version with and without the colvar module on.

When the colvar module is *off* (equilibrium MD), I get something like

Benchmark time: 256 CPUs 0.0268481 s/step 0.155371 days/ns 540.59 MB memory

When the colvar module is *on* (moving harmonic restraint on an RMSD
colvar calculated from 1981 C-alpha atoms), I get

Benchmark time: 256 CPUs 0.320515 s/step 1.85483 days/ns 569.555 MB memory

which is 11-12 times slower.

Is this the actual computational cost of a colvar calculation?

Also the scaling of this particular colvar calculation is not good:

Benchmark time: 48 CPUs 0.331787 s/step 1.92006 days/ns
Benchmark time: 128 CPUs 0.322472 s/step 1.86616 days/ns
Benchmark time: 256 CPUs 0.320515 s/step 1.85483 days/ns

Thanks in advance!


Dr. George Patargias
Postdoctoral Research Fellow
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27

Office: +302106597568

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