Michael Shirts wrote:
Hi, all-
I would like to add that for a constant temperature ensemble the effect
of this fix is neglegible.
It is only useful for constant NVE simulations.
Berk.
I think this might need some qualifications. If the constant
temperature dynamics are based inherently on NVE dynamics, they must
be affected similarly. For example, for Nose-Hoover thermostats,
there exists a conserved quantity. I would expect that this fix would
also improve that conserved quantity, wouldn't it?
One feature that would be useful is that for any algorithm that has a
"conserved energy-like" quantity, there should be an entry in the .edr
file with that quantity. It would be a useful check for algorithmic
consistency. I don't think this is yet in GROMACS, though I could be
wrong -- I haven't examined the CVS that recently.
How about total energy? In tends to be constant in NVE simulations. I
don't know what the conserved property would be in an NVT simulation.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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