Rescale Temperature when velocity of COM is not zero

From: Fred (Rui FENG) (fengruifree_at_gmail.com)
Date: Mon Jun 01 2009 - 15:12:05 CDT

Hi All,

I have a problem when I try to control the temperature.

Suppose we have a periodic box with atoms and Lennard-Jones force field
inside. When velocity of the center of the mass (COM) is zero, the output
temperature is the "real" temperature of the system. It's from the
equation: Ek = 3/2*R/n*T. When I rescale it by the "rescaleTemp and
rescaleFreq" parameters, the system temperature could be changed.

But if the velocity of COM is not zero, the output temperature consists of
two parts: the "real" temperature and the kinetic energy part (if we can say
it drift temperature). When I rescale it, both "real" temperature and
velocity of COM are changed.

So I was wondering if NAMD provides any parameters that only rescale "real"
temperature but don't change the velocity of COM? Thank you!

Have a nice day!

Fred

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