AMBER Archive (2009)

Subject: Re: FW: Solvent/solute ratio? Re: [AMBER] how to add desired number of water

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Fri Dec 11 2009 - 16:19:57 CST

> How *does* one estimate an appropriate amount
> of solvent for a given solute molecule in a MD simulation in explicit=20
> solvent?

My sense of it is, you want more than your cutoff, by some margin
to allow for box shrinkage during equilibration. For nucleic acids,
I have used 10A water (before adding ions) with 8A cutoff.

Bill

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