[gmx-users] Free energy sampling using G_bar

Fabian Casteblanco fabian.casteblanco at gmail.com
Thu Sep 15 17:16:40 CEST 2011

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:  fabian.casteblanco at gmail.com
-------------- next part --------------
A non-text attachment was scrubbed...
Name: H2.agr.tar.gz
Type: application/x-gzip
Size: 33237 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110915/7496a123/attachment.gz>

More information about the gromacs.org_gmx-users mailing list