AMBER Archive (2000)

Subject: initial density generated by solvatebox

From: Jake Isaacs (rjisaa0_at_pop.uky.edu)
Date: Mon Dec 18 2000 - 10:42:23 CST

Why does the solvatebox command result in an initial density of ~0.74 g/cc?
When I run a system solvated in this manner under constant pressure (1 atm)
it equillibrates to ~1 g/cc (expected water density at 1 atm). This also
results in the shrinking of my periodic box by about 5 Angstroms in all 3
dimensions. 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?

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            Jake Isaacs | Department of Biochemistry
        Phone: (859) 257-4706 | University of Kentucky
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