[gmx-users] Re: g_covar

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Mar 26 09:59:45 CET 2009


The covariances are defined as the second central moment, i.e. the
mean square displacement about the mean. Thus to make the PCA
interpretable straightforwardly, you'll need to calculate the
fluctuations with respect to the average structure.

This stands apart from fitting. The fit is performed to define the
conformational space, by removing translational and rotational degrees
of freedom. There you'll have freedom to choose the reference and the
fitting group, which will both have an influence on the results.
Especially when using different groups for fitting and for performing
the analysis, you'll have to make sure you know what you're doing, as
this can have an enormous impact on the results. The influence of the
reference used for fitting, assuming the same group is used for both
the fit and the analysis, shouldn't be too big.

Hope it helps,


On Thu, Mar 26, 2009 at 9:33 AM, Ran Friedman <r.friedman at bioc.uzh.ch> wrote:
> 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,
> Ran
> 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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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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