SHAKE convergence property for CUDA and nonCUDA NAMD

From: Jun Zhang (
Date: Wed Dec 08 2010 - 06:54:10 CST

Hello everyone:

I have just compiled CUDA version NAMD 2.7 and have been
testing its performence. It does speed up for at least 3.6
times than a non CUDA version on the same machine. However,
I have encountered a subtle issue and I cannot explain it:

    With the same input files (the same psf, pdb,
conf, and force field parameters), the non CUDA version runs
well, but the CUDA version, fails to converge for the SHAKE
algorithm. Only after I manually set the "rigidInterations"
to 2000 did work well. Since it is well known that SHAKE
algorithm has very good convergence property (usually less
than 20), this phenomenon seems somewhat strange. Does this
matter? By this I mean will such issue generate some
abnormal trajectory?
   I guess this may due to the different
algorithms of nonbonded interaction computation on CUDA and
nonCUDA version. But I am not sure. Does anyone have some
ideas on this problem? Thank you for your help.
Cheers up!

Jun Zhang
Nankai University



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