Yes, setting keep_files=2 in the &gen section of the MMPBSA.py input files
will allow you to keep all output files created by sander.
-Bill
2011/2/24 Jesper Sørensen <lists.jsx.dk>
> Hi,
>
>
>
> I want to make sure that I get all the output files from sander created for
> each frame.
>
> I love that MMPBSA.py will summarize the results for me, but for this
> system
> I need to make sure how many frames I can include, while also making sure
> that the frames are not correlated.
>
>
>
> Is it sufficient to run it with “keep_file=2” set in the input file? Will I
> get the output that I need then?
>
>
>
> I have found older papers that say to use frames every 20fs to 200fs, but
> that this is system specific.
>
> Is there a clever way to test this aside from block analysis?
>
>
>
> Best regards,
>
> Jesper
>
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--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Thu Feb 24 2011 - 04:30:05 PST
