[gmx-users] Energy Minimization Protocol for running Normal Mode Analysis

Anirban Ghosh anirbanzz at gmail.com
Fri Jun 29 07:05:44 CEST 2007

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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