Hello all, I am finished running a free energy calculation using g_bar and i followed Justin Lemkuls tutorial and I am in the process of analyzing inorder to determine if I had adequate sampling. I have read the 'BAR' paper by Bennett but there are still some concerns whether I have enough sampling (see attached). I see in the tutorial that the sampling goes up to very large sample numbers, some greater than 30,000 where mine only make it to about 300. This 'samples' refers to how many times a certain energy level was experienced? Does this mean my system should be left for longer times? My lines don't line as as closely as the Methane Decoupling tutorial do. Also, for other solvents that I used, some are giving me a warning for violating the 2nd law of thermodynamics and i noticed its because on one of the output lines, the entropy decreases a small bit, and some are giving me a free energy with a std deviation of at most 1.7 kJ/mol. Does this all mean my sampling is not enough?
Thanks for your help. -- Best regards, Fabian F. Casteblanco Rutgers University -- Chemical Engineering PhD Student C: +908 917 0723 E: [email protected]
H2.agr.tar.gz
Description: GNU Zip compressed data
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