On 6/15/12 6:53 AM, ms wrote:
Ok, I am using v-rescale now and the major artefacts seem to be gone, at least
on the very short term (2-3 ns).
It seems grompp should warn that andersen is not a good choice if you're using
CPUs :)
Such a warning would become outdated very soon - the 4.6 development version has
a proper implementation of the Andersen thermostat.
In the existing code for version 4.5.5, it seems the "Andersen" keyword is
accepted but there is no mention of its use in update.c or coupling.c,
suggesting to me that it's a ghost parameter that does nothing. There should be
some indication in the .log file that there might be a problem and/or problems
with the temperature should be apparent.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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