[Xplor-nih] noePot

[Charles at Schwieters.org]

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Hi Andreas--

> 
> >The energy function is defined as
> > 
> >        if pot=HARD or  r<rSwitch: 
> >                scale * r^hardExp
> >        pot=SOFT and r>rSwitch: 
> >                scale * (a + b / r^softExp + asympSlope * r)
> > 
> >        where
> >        b =  rSwitch^(softExp+1) * 
> >            (asympSlope - hardExp * rSwitch^(hardExp-1)) / softExp
> >        a = rSwitch^hardExp - b * rSwitch^(-softExp) - 
> >            asympSlope * rSwitch;
> 
> I calculated this potential as a function of r and the result is a potential 
> that is partially negative and that is not continuous at rSwitch. So i guess 
> this formula can't be the one which is used for the noe calculations. What is 
> the function used by the program?

I wonder what the problem is- I just plotted the curve with the
arbitrarily chosen parameters:
  hardExp=2
  softExp=1.9
  asympSlope=0.4
  rSwitch=2.3 
The resulting curve looks ok to me. Note that a and b are chosen such
that the potential and its first derivative match at rSwitch. So- the
program and docs look ok to me...

> 
> I wonder why the parameters in anneal.py differ so much from the default 
> values. What is the reason for this?
> 

actually, the values in eginput/protG/anneal.py are the same as those
set by create_NOEPot. The setup is included to illustrate how changes
might be made.
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