AMBER Archive (2009)

Subject: Re: [AMBER] Meaning of GMAX

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Mon Aug 24 2009 - 10:05:36 CDT

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_at_qtp.ufl.edu

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