> On Mar 8, 2015, at 11:18 AM, zahra khatti <zkhatti2000.yahoo.com> wrote:
>
> Dear amberists I need plot of binding free energy as a function of time.How can I obtain it with mmpbsa.py?
As Dave mentioned, equilibrium properties (like the free energy) are time-independent quantities. If what you are looking for is a “time series” (where the ‘time’ is merely an index of that particular data point -- not actually related to any real temporal definition), then you can use the “-do” flag to dump a CSV-formatted output file of all energies for all frames for the complex, receptor, and ligand.
The standard output of MMPBSA.py just gives you the mean and variance of these data sets. If you want to do more detailed analyses (like autocorrelation times or covariance analysis, for instance) then you need to use -do to write a CSV file and analyze the data from there.
This should be described in the MMPBSA.py section of the manual.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Mar 08 2015 - 19:00:03 PDT
