[gmx-users] eigenvalues as a function of time
L. Michel Espinoza-Fonseca
mef at ddt.biochem.umn.edu
Thu Feb 14 23:33:51 CET 2008
I have one more question. For example, if I have a trajectory of 10 ns
divided in intervals of 10 ps each, to obtain a set of eigenvalues
each 500 ps I have to calculate the eigenvalues using the following
Is that correct?
On Thu, Feb 14, 2008 at 2:54 AM, Marcus Kubitzki <mkubitz at gwdg.de> wrote:
> Hi Michel,
> I'm confused by what you mean by "splitting" the eigenvalues.
> With g_covar -b -e you can get eigenvals for a specified interval of
> time, e.g. 0-1ns. Getting eigenvals as a function of time (if that's
> what I suspect you want to do), you need to run g_covar for all
> intervals 0-t1, 0-t2, 0-t3, ... to get the desired sequence.
> L. Michel Espinoza-Fonseca wrote:
> > Hi all,
> > I have a MD trajectory and want to split the eigenvalues as a function
> > of time. I've been trying to do so with g_covar but with no success.
> > I'd like to know if you could guide me on this matter. I'm planning to
> > further used those values to calculate the entropy (By using Karplus'
> > approximation) vs time and its convergence in the simulation.
> > Cheers,
> > Michel
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> Marcus Kubitzki
> Max Planck Institute for Biophysical Chemistry
> Computational Biomolecular Dynamics Group
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