From: Gianluca Interlandi (gianluca_at_bioc.unizh.ch)
Date: Tue Sep 27 2005 - 14:42:43 CDT
Does anybody know what is best recommended to speed up the computation
with the least possible lost in accuracy:
1) SHAKE (rigidBonds all) & 2 fs timestep or
2) Multiple time-stepping algorithm: 1 fs on bonded interactions, 2 fs on
short-range nonbonded interactions, 4 fs on long-range nonbonded
interactions?
In the link below they show that 2) causes an energy drift although the
simulation results are qualitatively not altered:
http://www.ks.uiuc.edu/~sotomayo/private/answer.html
I have always used SHAKE & 2 fs timestep, like with the CHARMM code and I
have never seen an energy drift. Are there any arguments against the use
of SHAKE?
Many thanks,
Gianluca
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Gianluca Interlandi gianluca_at_bioc.unizh.ch
+41 (0) 1 635 55 93
+41 (0)79 655 73 35
http://biocroma.unizh.ch/gianluca/
PhD-Student of the Department of Biochemistry
at the University of Zurich Irchel, Switzerland
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