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
