"Normal" state variable fluctuation is a function of system size in MD; thus
for smaller systems, there is substantially more fluctuation than larger
systems. Dave Case has discussed this at least a time or two on the amber
reflector; I don't have pointers to the email or appropriate equations
handy, but the info is out there.
Regards - Bob Duke
----- Original Message -----
From: "Lei Jia" <leijia.nyu.edu>
To: <amber.scripps.edu>
Sent: Wednesday, October 17, 2007 7:46 PM
Subject: AMBER: Temperature fluctuation in NPT and NVE ensemble
> 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 - 06:07:20 PDT
