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
____________________________________________________________________
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:39 CST