Hi, i do some calculations with mainly noe restrained structures. Therefore i use a script based on the example script anneal.py. The formula for noePot according to the reference manual is:
>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 why the parameters in anneal.py differ so much from the default values. What is the reason for this? Thanks! Andreas _______________________________________________ Xplor-nih mailing list Xplor-nih@nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
