On Fri, Sep 23, 2011, hongphuc nguyen wrote:
> I have been trying to calculate Free Binding energy of my system ( 260
> residues and 1 ligand, 20 nanoseconds of MD simulation). However, I notice
> that the results are weird. I don't know whether the problem arises from my
> system or not. Attached here is graph of rmsd. input and output files are
> described as follows. Please give me some advice if you has encountered
> such a problem before. Thank you very much in advance.
There are all kinds of reasons why the rmsd would grow as a function of
time. This has nothing to do with your inputs to MM-PBSA, but rather is
a result of possible problems with the underlying simulation. Start by
visualizing the trajectory to get some idea of what is happening in a
structural sense.
....dac
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Received on Sat Sep 24 2011 - 06:00:05 PDT
