I found the reason for underestimating the electron density. When I wrapped
the hexagonal cell to an orthorhombic box, hid the waters and displayed the
periodic cells along the x and y axes, I saw there were gaps. In contrast,
when I wrapped to a parallelepiped box there were no gaps. However, the
Density Profile VMD plugin works only with orthorhombic boxes. Is it
possible to convert my hexagon to an orthorhombic box with "image"
directive of cpptraj?
thanks in advance,
Thomas
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Received on Tue Nov 19 2013 - 14:00:02 PST
