From: Arun Krishnan (krishnan_at_ttck.keio.ac.jp)
Date: Fri Nov 09 2007 - 02:08:39 CST
Dear All,
Please ignore my query.. I figured out how to do it. Sorry for the trouble.
Regards,
Arun
On Nov 9, 2007 4:24 PM, Arun Krishnan <krishnan_at_ttck.keio.ac.jp> wrote:
> Dear All,
>
> This might be a very simple question so please bear with me. How do I find
> the density of water in the water box?
>
> I found this answer in the archives:
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/2330.html
>
> in which it says: "I*f 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.*"
>
> Ok.. I got the number of water molecules from the pdb. Multiplied it by 18
> (molecular mass of water). How do I get the volume of the box?
> I think it is from the xsc file right? Do the a_x, b_y and c_z signify the
> dimensions of the x,y and z dimensions of the water box in nm?
>
> Would appreciate it if someone could kindly explain this.
>
> Thanks,
>
> Arun
>
>
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