VMD-L Mailing List

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Fri May 16 2008 - 03:29:41 CDT

Which program do you intend to use to create you truncated octahedron ?
If its AMBER, please note that the vectors described by Gromacs won't work.
If you do use AMBER to create your box, please check the AMBER mailing
list archives ... this issue has been discussed there

Best
vlad

George Madalin Giambasu wrote:
> 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
>
>
> 

-- 
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Dr. Vlad Cojocaru
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e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/
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