From: Webber (wpliao_at_gmail.com)
Date: Tue Aug 21 2012 - 03:46:25 CDT
(Sorry I have a weird feeling that this email was not received by the
mailing list (not showing up on the Mailing list webpage), thus sending it
again, if you have received it I apologise for the double posting and
please ignore this email, thank you)
After doing some more research on this topic I am starting to think that
outputting the gradient tolerance may be a feature that has been taken out
in recent versions (tutorial needs an update maybe?) and I guess that
explains why no one can answer my question...
If the energy gradient of iterations is not reported, may I ask how does
someone determine whether a minimization or MD calculation has reached a
level of convergence? I realise this may be a really silly question and MD
calculations may not use energy gradient as the measure of convergence...
If that is the case, what does a person write on a report or paper
regarding the criteria of stopping the simulations? Right now, all I can
think of is that "X was minimized with NAMD until the simulation reached
convergence" which I don't think is very nice to read....
Thanks for reading and all helps appreciated.
On 20 August 2012 10:02, Webber <wpliao_at_gmail.com> wrote:
> 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
> 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
> 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
> 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
> tolerance? Or maybe shed some light on where best to look?
> Much appreciated.
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