From: Webber (wpliao_at_gmail.com)
Date: Sun Aug 19 2012 - 19:02:29 CDT
Hi all,
I have been following the NAMD tutorial (ver: Feb 2012) to learn the basics
of
NAMD. When I was following the section on the output in the first chapter
(Basics of NAMD->Output: Water Sphere Log File, which can also be found at
http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node10.html
),
I found a discrepancy between the example log file, the portion of a log
file shown
on the tutorial page, and the log files I actually got. Both the example
log file and the
figure (fig 6) in the tutorial show lines describing the "initial step" and
the "gradient
tolerance", but these values are missing from my output. As the version of
the
tutorial is quite recent (Feb 2012), I don't think it is due to the version
of NAMD I use,
which is 2.9. (I also happen to have an older version (2.8) running on a
PPC, but
the output still doesn't have the values.)
Though I think I follow the tutorial and the configuration file to minute
detail, I
wonder if I am missing some important settings, such as some options or
flags
I should be eliciting NAMD with, or some default settings for NAMD.
Could someone please let me know how I can activate the display of the
gradient
tolerance? Or maybe shed some light on where best to look?
Much appreciated.
Regards,
Webber
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