Fabian Casteblanco wrote:
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
Sampling in the tutorial is excessive; I believe I state that in discussing the
free energy output settings.
how many times a certain energy level was experienced? Does this mean
Yes. The output histograms show the distribution of energy values in
neighboring windows.
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
The histograms look fine to me. Lots of overlap.
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?
Perhaps in this instance, yes, but not all of the sampling. You may have to
sample a bit more in the window that's causing problems, but likely not all of
them. I don't know whether uneven sampling (i.e. more points in one window
relative to others) is a problem for BAR.
-Justin
Thanks for your help.
--
Best regards,
Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E: fabian.castebla...@gmail.com
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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