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On 26/10/2011 11:04 PM, James Starlight wrote:
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cite="mid:CAALQopx+JohTYeaO=3cqB3s4pqGUXh5tS=gFSV04zqmJz4Qs_A@mail.gmail.com"
type="cite">Mark hello,<br>
<br>
<div class="gmail_quote">2011/10/26 Mark Abraham <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br>
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<div class="im"><br>
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We don't know the sense in which it "didn't minimize
properly," so there's not much point us guessing.
<div class="im"><br>
<br>
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<div>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 )<br>
<br>
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<br>
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<br>
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.<br>
<br>
<blockquote
cite="mid:CAALQopx+JohTYeaO=3cqB3s4pqGUXh5tS=gFSV04zqmJz4Qs_A@mail.gmail.com"
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<div>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? <br>
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<br>
Sorry, we can't make guesses based on things you can't remember
details about. Maybe you want to consider Essential Dynamics.<br>
<br>
Mark<br>
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