question about the influence of water box size in FEP

From: jieru.zheng_at_duke.edu
Date: Fri Mar 09 2007 - 09:30:40 CST

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Dear all,

I have a question about how to choose water box sizes in the FEP calculation. If
I choose different water box sizes for a FEP calculation, would be result be
different?

For example, within a thermodynamic cicle, two FEP calculations need to be done
in order to get delt_delt_G. However, if the two systems are of different size,
how should I choose the water boxes to get a good estimate? Or the water box
size really does not matter?

I could not find reference for this. Could anyone please help?

Thanks a lot!

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