From: George Madalin Giambasu (giambasu_at_gmail.com)
Date: Wed Aug 03 2011 - 11:18:10 CDT
Together with the Amber community I have put together a guide on how to
use Amber force fields in NAMD.
You can find it at:
The guide provides the following information:
1) A side by side comparison of many NAMD and Sander/PMEMD options,
2) How to get a better match between the energies and forces obtained
from NAMD and Sander/PMEMD.
3) How to set up truncated octahedron, rhombic dodecahedron and
hexagonal prisms periodic boxes.
4) How to use Amber tip4p water models in NAMD.
5) A NAMD/PMEMD benchmark.
I hope you will find it useful. Please let me know if you have any
questions and suggestions for improving the guide.
-- ____________________________________________________________________ Dr. George M. Giambasu Postdoc BioMaPS Institute and Dept. of gmgiambasu_at_biomaps.rutgers.edu Chemistry & Chemical Biology giambasu_at_gmail.com Rutgers University 610 Taylor Rd. Piscataway, NJ 08854-8087 USA ____________________________________________________________________
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