Mark hello, 2011/10/26 Mark Abraham <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 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? James
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