AMBER Archive (2003)

Subject: Re: AMBER: adding extra salt

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Fri Dec 12 2003 - 10:44:07 CST

> differences between
> first solvating the system and then adding ions versus first adding ions
> and then solvating the system? What do you recommend and a bit of why?

When leap adds ions to a solvated system, it finds a grid point
to add a water, then, rather than placing the ion on the grid
point and deleting all waters that have some overlap, it selects
the nearest water and replaces it with the ion. This gives better
packing, since deleting multiple waters creates voids.

Note that such voids are created around the solute anyway when
solvating, because waters are superimposed then ones overlapping the
solute are deleted - the partially-overlapping ones leave voids in
the non-overlap space.

Bill Ross

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