Re: [AMBER] MMGBSA of several MD trajectories

From: Carlos Simmerling <>
Date: Sun, 25 Jan 2015 09:49:52 -0500

If you're just averaging the snapshot energies, the results will be the
same. Split into as many files as you have processors for best efficiency.
This is if you're not using a packaged script to get a final energy, though
- in that case you'd need to modify it.
On Jan 25, 2015 9:31 AM, "James Starlight" <> wrote:

> 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,
> James
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Received on Sun Jan 25 2015 - 07:00:03 PST
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