Water density in the solvate plugin

From: David Cohen-Tanugi (dctanugi_at_mit.edu)
Date: Fri Jul 26 2013 - 10:50:20 CDT

Hello,

Is there a way to obtain the correct density of water using the
*solvate *plugin
in VMD?

If I create a solvation box whose dimensions are 30x30x30 using the
command:
*solvate -o waterbox -rotate -minmax {{0 0 0} {30 30 30}},*
the solvate plugin creates a box containing 2478 atoms, which equals 826
water molecules.

Meanwhile, the correct water density for a period box with dimensions
30x30x30 should be actually be 903 water molecules!

I am assuming that some edge effects are at play, but I would greatly
appreciate the community's help in solving this problem. Needless to say,
simulating water at the correct density is an essential requirement for
many fields of research.

Best,
David Cohen-Tanugi
Materials Science & Engineering, MIT

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