AMBER: Temperature fluctuation in NPT and NVE ensemble

From: Lei Jia <>
Date: Wed, 17 Oct 2007 19:46:29 -0400

Dear Amber community,

We are studying protein/DNA complex structures with MD simulations. We carried out simulations under the NVE ensemble with AMBER 9 PMEMD. The temperature vs time plot shows that the temperature fluctuates about 5 degrees plus/minus the initial temperature which is 310K. Our old experience with the NPT ensemble running with AMBER 8 showed the temperature only fluctuates about 1 degree plus/minus the setting temperature due to the close coupling in the thermo-bath.

Is the 5 degrees fluctuation a kind of reasonable range in the NVE ensemble?

Thank you in advance for your help.

Lei Jia, Ph.D.
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Received on Sun Oct 21 2007 - 06:07:17 PDT
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