AMBER Archive (2000)

Subject: Re: docking

From: Andreas Svrcek-Seiler (svrci_at_tbi.univie.ac.at)
Date: Thu Oct 05 2000 - 11:48:46 CDT

Hi,
>
> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
> MD production, tautp=0.2, taup=0.2

sorry i can not answer your question, but if the line above means that
you run a 'production run' of a MD with tautp=0.2,
you should be warned, the berendsen method (especially with tautp small)
can produce bad artefacts. i.e. it tends to freeze out the highest
frequency eigenmodes of your system und to pump the kinetic energy
into the lower frequency eigenmodes. for details see
"The Flying Icecube: Velocity rescaling in Molecular Dynamics Leads to
Violation of Energy Equipartition", Harvey et al., Journ. Comp. Chem.
 19,7, 726-740.

best regards, greetings from vienna
Andreas

             
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