From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Mar 15 2007 - 12:25:44 CDT
Hi Liguo,
there are probably two issues here. The first is that the TIP3 water
model does not give a density of 1.0 g/cm3, but rather something along
the lines of 0.98. This is roughly what you should get from the
simulations. I've never seen anything as low as 0.9, so I also have to
ask, how did you calculate your volume for doing the density
calculation? Did you use measure minmax $sel in VMD or take the volume
from the side lengths of an NPT simulation? Using measure minmax will
not give you the correct volume because the surface is irregular...
Peter
Liguo Wang wrote:
> 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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