Hi,
> 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).
Please note that at the moment you can not combine BAR analysis with
softcore potentials, this will be fixed soon...
> But my questions is, how to process such data? I try the python script in
> "A Python implementation of the
If you want to use Michael Shirts python implementation of MBAR, you have
to convert Amber output to pymbar input. The attached script may be a good
starting point for this.
Kind Regards,
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Thu May 12 2011 - 01:00:02 PDT
