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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. -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.5 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> iD8DBQFE8v2kPK2zrJwS/lYRAlU3AJ9GJfDrMVpOcw155N2GxxfLUNtJWACfVIGw 2IwyZR/kJqpVIcG4NBufsfo= =qcQ+ -----END PGP SIGNATURE-----
