[AMBER] MMGBSA of several MD trajectories

From: James Starlight <jmsstarlight.gmail.com>
Date: Sun, 25 Jan 2015 15:31:31 +0100

Dear Amber Users,

I need to calculate dG of protein-small ligand binding using MMGBSA method
from two independent 50ns trajectories to obtain better statistics and
reduce entropy error from its under-sampling. I wounded to know based on
the additivity of the MMGBSA whether it will be better to make 1 MMGBSA
calculation from both merged trajectories (2x ensemble) or alternatively
perform 2 independent MMGBSA for each trajectory (which might be longer in
computation time)? Which of the alternatives might be better?

Thanks for help,

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Received on Sun Jan 25 2015 - 07:00:02 PST
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