heat diffusion

From: Jonathan Lee (jonny5_at_rice.edu)
Date: Wed Jun 20 2007 - 17:39:22 CDT

Hello all,
   I am trying to do the heat diffusion computation from the tutorial
(section 2.2.1) but with some changes. Instead of a water sphere with
spherical boundary conditions, I would like to use a water box with
periodic boundary conditions (and cooled bath on two opposite ends). I
have been having problems where the temperature of the system rises
instead of falls (my bath temperature is 200K and initial system
temperature is 300K). I also sometimes get the error "Periodic box is
too small."
   To begin, could somebody please confirm the changes that I should
make to the following file from the tutorial:
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-files/2-6-heat-diff/ubq_cooling.conf

1) Of course, change all the filenames and directories to the
appropriate ones
2) Change the first line of the PBC to "if { 1 } {" and change the
values of the periodic cell appropriately
3) Change the first line of the spherical BC to "if { 0 } {" or delete
altogether
4) Should I turn on PME? I think it was causing problems for me, so I
left it off
5) Should I turn on Constant Pressure Control?

Also, what could possibly cause a system's temperature to rise
abnormally (it reaches 400-800K!)? Thanks.

Jonathan

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