On 26/10/2011 11:04 PM, James Starlight wrote:
Mark hello,
2011/10/26 Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@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.
Mark
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