Am 02.04.2009 um 12:42 schrieb Rainer Bockmann:
the difference is probably due to thermal coupling: with Berendsen
thermostat, Gromacs versions 3.3.3 to 4.0.4 yield similar results.
In contrast, using v-rescale, results using version 4.0.2 are
significantly different from 4.0.3 or 4.0.4 results.
Are you using freeze - groups and are your initial velocities to small?
Best
Martin
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