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" <jmsstarlight.gmail.com> 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
