online guide for using amber ff in NAMD

From: George Madalin Giambasu (giambasu_at_gmail.com)
Date: Wed Aug 03 2011 - 11:18:10 CDT

Hello namd-list,

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:
http://ambermd.org/namd/namd_amber.html

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.

George

-- 
____________________________________________________________________
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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