Re: How to get information of computing time for LJ calculation and pair list generation

From: Chris Harrison (
Date: Wed Mar 17 2010 - 00:06:07 CDT


This capability is not available in the general release. You could get
timings if you are willing to add the appropriate code and recompile namd.

Let me know if you need further help.


Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                            Voice: 217-244-1733               Fax: 217-244-6078
On Mon, Mar 15, 2010 at 12:15 PM, Hideya Nakamura
> Dear NAMD users,
> I am doing NAMD simulation to compare computing performance of NAMD
> with our MD implementation.
> I want to know the computing time for LJ calculations and pair list
> generation in NAMD.
> I found some lines in .log file, however, they seem to show computing
> performance of whole MD implementation.
> Could someone please tell me how to get information of computing time
> for each calculation part??  Thanks
> __________________________________________________________________
> Hideya Nakamura, Ph.D.
> Post Doctoral Associate
> University of Florida, Particle Engineering Research Center (PERC)

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