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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