On 12/24/10 6:40 PM, ms wrote:
On 24/12/10 12:26, David van der Spoel wrote:
I'm not an expert, but isn't Berendsen usually not used because it
doesn't give a correct ensemble? I may be partial because I personally
know Giovanni Bussi, but it seems from what I've heard that v-rescale is
the best choice usually.
V-rescale is a good choice. Berendsen not only gives you the wrong
ensemble but it also biases the energy distribution to lower energies.
Out of curiosity: why is it still supported in GROMACS? Wouldn't lead to
less confusion if it is removed? :)
It's still useful for equilibration, e.g. gas to liquid conversion.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
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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