[AMBER] more on the Berendsen thermostat

From: David A Case <david.case.rutgers.edu>
Date: Wed, 23 Nov 2016 13:44:29 -0500

OK: late-onset dementia is fuzzing my brain. Here is corrected info on
the problem I recently saw with a protein-water simulation. Parameters
were ntt=1, tautp=100., dt=0.001. [In my experience, short time steps are
needed to get reasonable energy stability in NVE.]

RMS vs time is in the attached plot. The correction from my previous post is
that the bad behavior happens at 0.8 microsec, not 8 microsec. Another
caveat: I plan to re-run with ntt=0, to get more evidence that ntt=1 is really
to blame, but to me it looks likely.


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Received on Wed Nov 23 2016 - 11:00:05 PST
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