[gmx-users] Re: Diagonalizing matrix (g_covar)

Mark Abraham mark.j.abraham at gmail.com
Wed Feb 20 12:54:39 CET 2013

On Tue, Feb 19, 2013 at 8:19 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Seok Yun,
> Duh. I meant why are you trying to determine the eigenvectors and
> eigenvalues of a 50k by 50k covariance matrix. How did you end up with
> such a matrix, and why do you think that that matrix will help you
> solve your problem? What is your problem? What is the question you're
> trying to answer? And does it need to be so complex? Maybe the
> solution is not including the solvent, or not including the hydrogens,
> or only including backbone, or only using C-alpha.

Or fewer trajectory frames, depending what g_covar is operating on.

As always, providing at the start all the relevant information you can
think of will help you get a better answer. The people who help by giving
free advice can do that better and faster if the people needing help
participate well!


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