Dear Amber users,
How to calculate the distance between the nearest atoms in periodic boundary conditions for polymer structure in truncated octahedron solvent box. Here is the fortran code I used for polymer in rectilinear solvent box, how do I modify it for truncated octahedron.
xc = x(center of polymer)
yc = y(center of polymer)
zc = z(center of polymer)
do i=1,natm
x(i)=x(i)-xc
x(i)=x(i)-bx*dnint(x(i)/bx)
y(i)=y(i)-yc
y(i)=y(i)-by*dnint(y(i)/by)
z(i)=z(i)-zc
z(i)=z(i)-bz*dnint(z(i)/bz)
Any help is greatly appreciated.
Thanks,
Ashar
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Received on Wed Mar 11 2015 - 08:30:03 PDT
