[gmx-users] Normal Mode Analysis

Mark Abraham Mark.Abraham at anu.edu.au
Wed Oct 26 14:09:54 CEST 2011

On 26/10/2011 11:04 PM, James Starlight wrote:
> Mark hello,
> 2011/10/26 Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>>
>     We don't know the sense in which it "didn't minimize properly," so
>     there's not much point us guessing.
> The output value for Epot was -2.0 after steep minimization and -2.5 
> after CG. Also as the consequense after both energy minimization runs 
> the system told me that the system have not been minimized completely 
> or the step size was too short ( I've changd the step size from 0.01 
> in both directions as well as EMtool from 1000 to 0.1 but that results 
> were unchanged )
> Also during diagonalization of the Hessian the system told me that 
> lowest six modes were not zero's in their frequensies. It's also could 
> indicate that I've analyzed not properly minimized structure

Or that your starting structure is not close enough to a sensible 
minimum for a local gradient-based optimizer to do the job. Look at the 
atoms with the large forces and see what you can learn.

> By the way I've heard that there is possible way to extract Normal 
> Modes from MD trajectories directly. E.g I've simulated my protein and 
> obtain trr file and want to extract from that trajectory all 
> eigenvectors ( modes) separately. Might it be realized in Gromacs and 
> via what program should I do it?

Sorry, we can't make guesses based on things you can't remember details 
about. Maybe you want to consider Essential Dynamics.

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