[gmx-users] Re: g_covar

Ran Friedman r.friedman at bioc.uzh.ch
Thu Mar 26 09:33:50 CET 2009

Dear Dagoberto,

Choosing the right protein structure (and also which part of the protein
to align) depends a lot of your system. I wouldn't use an average
structure for a system that's changing a lot, because it may not be
representative. It's hard to provide a more elaborate answer without
many details about your system and what you're trying to simulate. It
can be helpful to read both on the methods of covariance analysis and on
some implementation - i.e., papers in which it has been used to
calculate correlated motion.

As to modification of the code, I found it easiest to compile the source
code for various tools within GMX. It's not necessary, but it makes your
life easier.

Since your question doesn't refer to the modified g_covar code directly,
I'm ccing the gromacs mailing list. Please keep future correspondence there.

Good luck,

darmenta at ibt.unam.mx wrote:
> Dear Ran friedman
> I'm actually biochemistry student and I'm using your uploaded version of g_covar
> in order to calculate correlated motion. I have c-alpha trajectory of 50 ns
> simulation that describe the functional movement of my protein, but the
> trajectory are not in the equilibrium. My questions are,  what reference
> structure I must use in order to calculate correlated motion?, could I use the
> average structure as reference?
> In the other hand, Im doing some modifications to the g_covar program and I want
> to know the way to compile it. Is necessary to compile within gromacs?   What is
> the easiest way?
> I would appreciate any help in this matter.
> Dagoberto Armenta Medina
> ----------------------------------------------------------------
> Este mensaje fue enviado desde el servidor Webmail del Instituto de Biotecnologia.

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