# Re: [AMBER] Truncated octahedron

From: Bill Ross <ross.cgl.ucsf.edu>
Date: Wed, 11 Mar 2015 08:35:36 -0700

You could look for amber code that does the same thing.

Bill

<div>-------- Original message --------</div><div>From: Arjun Sharma <arjunsharma83.gmail.com> </div><div>Date:03/11/2015 8:24 AM (GMT-08:00) </div><div>To: amber.ambermd.org </div><div>Subject: [AMBER] Truncated octahedron </div><div>
</div>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 - 09:00:03 PDT
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