Water density in the solvate plugin

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


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
*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.

David Cohen-Tanugi
Materials Science & Engineering, MIT

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