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

Mark Abraham mark.abraham at anu.edu.au
Sun Jul 1 10:41:33 CEST 2007

> 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.

You asked this question on Friday
http://www.gromacs.org/pipermail/gmx-users/2007-June/028298.html and got
two answers pointing you in useful directions (follow the links from that
page). People posting repeat questions lose credibility fast around here.


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