Re: Water density in the solvate plugin

From: Axel Kohlmeyer (
Date: Fri Jul 26 2013 - 10:58:57 CDT

On Fri, Jul 26, 2013 at 5:50 PM, David Cohen-Tanugi <> wrote:
> 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.

you simply *must not* expect to get the correct density from such a procedure.
if you'd enforce the correct density, you get overlaps, bad contacts
and many bad things will happen because of that.
what you *have* to do, is to follow a proper equilibration protocol.
*and* you have to make a choice: a) do you want to have the "natural
density" of the water potential that you are using or b) do you want
to have a specific density.
in the first case, you run with an NPT ensemble after the
initial-minimization and brief const volume run and wait until your
system has reached a stabilized density.
in the second case you do the same, but then rescale the box to your
liking and the desired density and then keep equilibrating in NVT


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

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

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