**From:** LEWYN LI (*ll2150_at_columbia.edu*)

**Date:** Fri Jun 10 2005 - 22:22:42 CDT

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Dear Leonardo,

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!

LEWYN

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
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*> calculate the density of water during a simulation. Someone knows if
*

*> there is a way vmd can give that information???
*

*>
*

*> thanks
*

*>
*

*> Leonardo
*

*>
*

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