From: Jonathan Lee (jonny5_at_rice.edu)
Date: Fri Jun 22 2007 - 11:36:55 CDT
Can anybody help me with this? Thanks.
Jonathan
Jonathan Lee wrote:
> 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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