[gmx-users] How to proceed with energy minimization for Normal Mode Analysis

[Anirban Ghosh]

Hi,
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.

Regards,


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

 				
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