online guide for using amber ff in NAMD

From: George Madalin Giambasu (
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:

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
    Chemistry & Chemical Biology
Rutgers University                     
610 Taylor Rd.                    
Piscataway, NJ 08854-8087   USA        

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