AMBER Archive (2007)

Subject: AMBER: temperature artifacts with andersen and GB?

From: David Mobley (dmobley_at_gmail.com)
Date: Wed Apr 11 2007 - 11:50:17 CDT

All,

I know the manual highly recommends using Langevin for temperature
control when using GB, but I insisted on trying Andersen anyway while
simulating a small molecule. I find that the average temperature (in
vacuum, or in GB solvent) is consistently too low (i.e., average of
250K over 500000 steps, when thermostatting to 300K, with vrand=500).
Looking at the instantaneous temperatures from the energy file, which
I'm writing every hundred steps, I find that immediately after every
randomization, the "temperature" spikes to about 2800K, then wobbles
around somewhere in teh 100-250K range until the next randomization.

I'm now going to Langevin, which seems to be working fine. But I don't
see any reason why the Andersen thermostat should give this behavior,
so it might be worth looking into.

Thanks,
David
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