From: Jonathan Lee (jonny5_at_rice.edu)
Date: Fri Jun 15 2007 - 17:40:52 CDT
I have some questions about the heat diffusion calculation in the
NAMD tutorial (page 53).
1) The shell is maintained at a temperature of 200, right? (As opposed
to just initialized to 200.)
2) What is the temperature that is output (step 11, page 55)? Is that
the temperature of everything excluding the 200K shell?
3) It seems to me that the calculation should take into account the
inner radius of the shell. If the radius is much larger, shouldn't it
take a longer time for the diffusion to occur?
4) Can I do a similar calculation but with a rectangular prism domain
(i.e. fix the temperature at one end and calculate the heat diffusion to
the other end of the box)?
Basically, my understanding is that the temperature should be maintained
in one region and measured in another region a finite distance away.
That distance (and the time of diffusion) should be taken into
consideration when finding the diffusivity. Am I overlooking
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