From: LEWYN LI (ll2150_at_columbia.edu)
Date: Fri Jun 10 2005 - 22:22:42 CDT
If you used periodic boundary condition for a cubic water box, the
density will remain constant and all you need to do is to determine the
total number of water molecules (the pdb will tell you that), multiply it
by the molecular mass of water, and then divide it by the volume of the
box to get the density in g/L.
If you were using some other type of water boxes, such as a water
sphere, then the problem is trickier. I suppose you could try to estimate
the radius of the sphere using vmd (Mouse -> Label -> Bond). Select two
water molecules at the opposite ends of the sphere and vmd will tell you
the distance. This will be a rough estimate of the diameter. You can
proceed to estimate the volume.
There are probably more accurate and sophisticated ways to do
this, but I don't know them off the top of my head.
Hope this helps!
On Fri, 10 Jun 2005, Leonardo Sepulveda Durán wrote:
> Hello list!!!
> I searched into namd and vmd manuals and I have not found a way to
> calculate the density of water during a simulation. Someone knows if
> there is a way vmd can give that information???
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