[gmx-users] eigenvalues as a function of time

[L. Michel Espinoza-Fonseca]

Mark,

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
intervals:

0-500 ps
501-1000 ps
1001-1500 ps
....
9501-10000 ps

Is that correct?

Thanks!
Michel

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.
>
>  Marcus
>
>
>
>
>  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
>  Am Fassberg 11
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