**From:** Jonathan Lee (*jonny5_at_rice.edu*)

**Date:** Mon Jun 18 2007 - 12:16:20 CDT

**Next message:**Raul Araya Secchi: "Normal mode analysis"**Previous message:**Carsten Olbrich: "Differences between 32bit and 64bit version of NAMD?"**In reply to:**Jonathan Lee: "heat diffusion calculation"**Next in thread:**QJos=E9_R=2E_Sabino=22?=: "Re: Re: heat diffusion calculation"**Reply:**QJos=E9_R=2E_Sabino=22?=: "Re: Re: heat diffusion calculation"**Reply:**Victor Ovchinnikov: "Re: Re: heat diffusion calculation"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Anybody? Thanks.

Jonathan

Jonathan Lee wrote:

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