On Tue, Apr 20, 2021, Vaibhav Dixit wrote:
>This seems like a very large number of frames and thus bring some questions
>to mind.
>At present I have 2000 frames for a 40 ns simulation, thus what would you
>recommend?
I don't think it's very feasible to use quasiharmonic calculations to
estimate entropy on a 234-residue protein. It's probably possible to make
some approximations (e.g. don't compute all the modes), but this would be a
research project in itself, and one would need to understand in detail what
quasiharmonic calculations are doing.
>Also, it will be helpful if you can suggest how to troubleshoot the mode
>calculation especially in the absence of useful error messages.
Please re-read the opening paragraphs of the MMPBSA.py chapter, especially
the part in bold-face type. Also, I can't remember if you confirmed that
you looked in all the output files to find possible error messages.
...dac
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Received on Tue Apr 20 2021 - 05:00:02 PDT
