Re: AMBER: Does amber use water density around 1 at room temperature

From: Thomas Steinbrecher <>
Date: Wed, 24 Jan 2007 15:26:50 -0800 (PST)


> Dear Ross,
> Thank you for your kind help. But I am still confused. As you mentioned,
> amber used TIP3PBOX etc having been equilibrated to have approximately
> 1g/cm3. So that if I used "solvatebox" command to solvate an "empty" unit, I
> think the density should still be around 1, isn't it?

my comment on what you might see will be illustated by putting a 0 A
solvent layer around the TIP3PBOX:

> solvatebox TIP3PBOX TIP3PBOX 0
   Solute vdw bounding box: 18.774 18.774 18.774
   Total bounding box for atom centers: 18.774 18.774 18.774
   Solvent unit box: 18.774 18.774 18.774
   Total vdw box size: 22.296 22.002 22.520 angstroms.
   Volume: 11047.470 A^3
   Total mass 3891.456 amu, Density 0.585 g/cc
   Added 0 residues.

You see that leap generously adds an additional vdw-layer of 3.5 A around
the edges of your solvated system. As you see 18.7^3 / 22.3^3 is 0.589, so
the gain in volume explains the low density you see.

The TIP3PBOX with a side length of 18.774 has a density of

216 *18 amu / 6617 A^3 which is ~ 1g / cm^3



Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA

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Received on Sun Jan 28 2007 - 06:07:12 PST
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