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

[Mark Abraham]

> 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.

Check out links from
http://wiki.gromacs.org/index.php/normal_mode_analysis. You will probably
want double-precision optimization.

If you know enough to observe it's in a local minimum, then you should
change some aspect of the structure to get it out of the minimum...

Mark