Re: [AMBER] Truncated octahedron

From: Crowley, Michael <>
Date: Wed, 11 Mar 2015 15:39:03 +0000

Do the same thing but in fractional coordinates, then convert back to
Use the information at the end of the coordinate/restart file for box
sizes and angles.

Michael F. Crowley, Ph.D., Principal Scientist
National Renewable Energy Laboratory
15013 Denver West Parkway, MS 3323
Golden, CO 80401
303-384-6345  office
303-887-0149  mobile
On 3/11/15 9:24 AM, "Arjun Sharma" <> wrote:
>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.
>AMBER mailing list
AMBER mailing list
Received on Wed Mar 11 2015 - 09:00:04 PDT
Custom Search