You can go into the code and do this of course, that is why amber is
distributed with its source code.
Now, think what this will look like for a really large system. For each
atom, you would have a single entry. And this will carry for each time
you print. This is quite a bit of data !
The way we use GMAX is basically to see if there is a particular atom
making a bad contact. If the identity of the GMAX atom changes, then it
is 'distributed' and much less of a worry.
Adrian
Ashish Runthala wrote:
> I need to ask a very basic doubt here, if you don't mind. Correct me if i am
> wrong about it.
> We always try to remove the higher values of GMAX and we also wish to keep a
> lower value of RMS for better results.
> But i saw only a single highest value of GMAX. Many a times, i saw other
> incidences where other values have also resulted at GMAX less than the
> earlier ones. So why dont all such values as compared to the mean and
> standard deviation of the other normal or lower values can be considered
> with their positions being displayed in the output file. I guess it will
> help in overall refinement, instead considering a single value.
>
> Ashish
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>
--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project
Department of Chemistry
Senior Editor. Journal of Physical Chemistry
American Chemical Society
University of Florida PHONE 352 392-6972
P.O. Box 118435 FAX 352 392-8722
Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
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Received on Mon Aug 24 2009 - 11:11:31 PDT
