[gmx-users] Normal Mode Analysis

[James Starlight]

Mark,

2011/10/26 Mark Abraham <Mark.Abraham at anu.edu.au>

>
>  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.
>
So for that purpose I've done steep minimization first and only that based
on that minimized structure I did CG minimization. I changed the emtool (
from 100 to 1000) as well as step size but my structure always have not been
prorely minimized ( based on the system output ). Also I've found that there
is third L-BFGS
<http://www.gromacs.org/Documentation/Terminology/L-BFGS>algorithm for
minimization. In what cases this minimization could be
helpfull?



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

As I know the Essential dynamics is the type of the PC analysis ( in this
case the ensemble of the analysed structures is replaced by the ensemble of
the MD snapshots ). But I've heard that there is possible ways to extract
normal modes indirectly from the output trajectories.


James
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