Re: Truncated Octahedron for VMD and NAMD simulation

From: George Madalin Giambasu (
Date: Thu May 15 2008 - 15:23:51 CDT

1) Check out the Gromacs manual for how to specify the vectors of the
unit cell for the truncated oct.
2) Make an estimate on how big the length of an edge of the oct. would
be, enter the values of the cell vectors in an Namd configuration file
and let your system equilibrate with NPT for a 1-2ns. Specify
"wrapnearest on" and, in the end, you will get truncated oct. shaped sytem.

I hope this helps,


George Madalin Giambasu                        PhD Student
University of Minnesota                        Phone : (612) 625-6317
Department of Chemistry                        Fax   : (612) 626-7541
207 Pleasant St. SE                            e-mail:
Minneapolis, MN USA 55455-0431       
York Research Group                  

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