Re: [AMBER] System temperature

From: case <>
Date: Sun, 19 Jun 2011 10:30:43 -0400

On Fri, Jun 17, 2011, Jason Swails wrote:

> Another idea, though it may require careful thinking about, is to 'trick'
> the system into heating different atoms differently simply by changing the
> masses of certain atoms....

No: this won't work. The partitioning of energy and Boltzmann (equilibrium)
populations of conformers are not affected by atomic masses. You'll end up
with a system of uniform temperature, but atoms with non-physical masses would
be either too sluggish or not sluggish enough.

Note that (a) there is no "correct" way to have multiple temperatures, since
this is an unphysical and non-equilibrium constraint; (b) you will have to
play around some, since it is not clear that setting ntt=1 or 3, and just
using different target temperatures for different atoms will really work. You
should probably do some literature search to see what others' experience
is--I'm pretty sure ideas along these lines have been tried before.


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Received on Sun Jun 19 2011 - 08:00:03 PDT
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