Why is water density not 1.0g/cm3?

From: lw257_at_email.med.yale.edu
Date: Wed Mar 14 2007 - 18:57:06 CDT

Dear NAMD users,

I tried to study peptide in a water box and found out that the water density was
just 0.85g/cm3. So I set up a pure water box (40A*40A*40A), minimized the energy
and run the NPT simulation for 10ns. The averaged water density was 0.9g/cm3.

Then I calculate the water density from the wat.pdb which is used by solvate
package to put water molecules around proteins. Surprise! The density is still
0.9g/cm3, instead of 1.0g/cm3. Did anyone see similar problem? Or did anyone
get the correct water density using NAMD?

Thanks.

Liguo

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