AMBER Archive (2000)

Subject: Re: initial density generated by solvatebox

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Dec 18 2000 - 11:23:04 CST

        Why does the solvatebox command result in an initial density
        of ~0.74 g/cc?

Superimposing a box of water on te solute & box leads to
vdw voids since packing is not achieved.

        If I want about 10 A of clearance on all sides of my solute, is
        the only way to correct this situation to initially solvate with 12.5 A
        clearance?

Yes.

Bill Ross