[Xplor-nih] noePot

[Andreas Ceymann]

Hi Charles,

On Monday 28 August 2006 16:28, you wrote:
> 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...

Thanks for the help! I added brackets by mistake, so my plot was wrong. I 
checked it several times before posting, but missed that.

>
> > 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.

It is just the documentation in the internet that is not up to date:

 "The following parameters can be set [defaults in square brackets]
 
  nMono      - number of monomers [1]
  verbose    - if true, sporadically spit out info [False]
  scale      - scale factor
  aveExp     - exponential to use in sum averaging [6]
  dOffset    - potential offset [0]
  hardExp    - exponential in hard region of potential [2]
  rSwitch    - distance at which to switch from hard form [10]
  softExp    - exponential in soft region of potential [2]
  asympSlope - slope in linear asymptotic region of pot [0]
  threshold  - threshold in violation calculation [0.1]
  potType    - type of potential: "soft" or "hard" [hard]"

I guess i will not use this documentation any more and look up everything 
directly in the scripts. The docu is quite confusing!

Best regards!
Andreas