AMBER Archive (2007)

Subject: AMBER: Temperature fluctuation in NPT and NVE ensemble

From: Lei Jia (leijia_at_nyu.edu)
Date: Wed Oct 17 2007 - 18:46:29 CDT

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.
Biology_at_NYU
212-998-8228
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