Hi all,
I just finished the tutorial about the MM/PB(GB)SA method with my
complex. All is fine and using cuda, after some optimizations, the
calculations could be launched on a workstation. I have just few general
questions, reading the literature, one can found for similar complexes
very different lengths of production run, from few ns to 1000 ns. I
imagine that the error decrease with the length of the run and the
number of frames but are there general/reasonable parameters? or each
user should test different length of MD production before incorporating
mutations etc.?
Also, I found the tutorial to decompose the free energy contributions of
each residue (quite redundant with the ala-scan?), but it seems to be
appropriate only for amber11?
https://ambermd.org/tutorials/advanced/tutorial3/py_script/section6.htm
Thanks,
Best regards,
Baptiste
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Received on Thu Feb 06 2020 - 03:30:02 PST
