Hi,
hm, you should get a simple cycle like this to close to within 1 kcal I
would assume. Are the numbers you present values from full TI cycles with
two transformation legs each? (although even if not, the cycle should
close) Do you do 1-step or 3-step transformations?
The likely conclusion is that (one of) your simulations is not converged.
Are all the dvdl curves flat, free of kinks and possessing small error
bars? No sudden conformational changes from one window to the next? All
starting structures are similar? You do not by any chance have differing
partial charges for the same compound in two calculations?
You can also look at the dvdl autocorrelation times to check if some
windows are slow to converge.
Maybe something of this works...
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Mon May 13 2013 - 10:00:02 PDT
