[gmx-users] Energy Minimization Protocol for running Normal ModeAnalysis

Josiah Zayner jz75596 at appstate.edu
Fri Jun 29 19:52:58 CEST 2007

Ming & Wall (2005) Quantifying Allosteric effects in Proteins. PROTEINS:
Structure, function and bioinformatics



They perform normal mode analysis for enzyme/apo-enzyme. Gives brief of
preparation for analysis.


Josiah Zayner




From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Anirban Ghosh
Sent: Friday, June 29, 2007 1:06 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] Energy Minimization Protocol for running Normal


I am new to GROMACS. I want to perform Normal Mode Analysis of a protein.
For that I require a well minimized structure. I have minimized my structure
using steepest descent and conjugate gradient. But the structure seems to
have got struct in a local energy minima. How should I proceed to get a well
minimized structure in order to go for Normal mode Analysis? 
Please suggest any protocol.


Anirban Ghosh
M.Tech Bioinformatics 
University of Hyderabad
Hyderabad - 500 046
Andhra Pradesh

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