[gmx-users] Normal Mode Analysis

James Starlight jmsstarlight at gmail.com
Wed Oct 26 14:04:36 CEST 2011

Mark hello,

2011/10/26 Mark Abraham <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

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

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