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.NYU
212-998-8228
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Received on Sun Oct 21 2007 - 06:07:17 PDT
