Dear Amberer's
I can calculate solvation free energy by TI in amber11, but would like to
try Bennett acceptance ratio
(BAR) method.
I set ifmbar=1 in the input file as the Amber11 user manual indicates, so
that sander.mpi can collect potential
energy in simulations. In TI simulations, the lambda for each simulations
are 0.1 0.2 ...0.9, and in each
simulation, total potential energy of the system as it would be for
different l-values (0.1 0.2 ...0.9)
are collected (just use default bar_l_min bar_l_incr etc).
But my questions is, how to process such data? I try the python script in "A
Python implementation of the
multistate Bennett acceptance ratio", but just get some strange results.
Do I have to write the code to process data myself? Any suggestion or
comment is very welcome.
Thank you so much for your kind help.
xiaodong huang
Research School of Chemistry
ANU
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 11 2011 - 22:00:03 PDT
