What Dan just described was how you can obtain a Na+
3D-distribution-function whose values are divided by the bulk Na+
density. This will be helpful when you want to locate the regions in
space that are surrounded, for example, by iso-surfaces with iso-values
of 2-times the bulk density, as you will have to choose simply an
isovalue of 2.0 in whatever graphical program you use (vmd, chimera, etc).
To convert Molar (mols/L) units into densities (particles/A^3) as
cpptraj needs you just have to scale the the value of the molar
concentration by 6.023 * 10^-4 .
best,
George
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Received on Wed Jul 26 2017 - 12:30:02 PDT
