[gmx-users] Strong egative energy drift (losing energy) in explicit water AMBER protein simulation [SOLVED]
Justin A. Lemkul
jalemkul at vt.edu
Fri Jun 15 13:02:39 CEST 2012
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Such a warning would become outdated very soon - the 4.6 development version has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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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