[gmx-users] Re: g_covar

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Aug 16 12:31:55 CEST 2011

Hi Gideon,

Maybe you want the atomic matrix produced by g_covar -xpma?



2011/8/16 גדעון לפידות <glapidoth at gmail.com>:
> Thanks for your replies.
> I would like to clarify regarding my first questionn. I don't want a g_dist
> matrix. I would like to get a covariance matrix where the values correspond
> to absolute distance and not dived into different dimensions. for example
> say I have a protein with 100 aa and I run g_covar only on Ca I'll get a
> 300X300 covariance matrix instead of a 100X100 matrix which is what I want.
> is there any built in command in Gromacs that will give me this?
> Thanks,
> Gideon
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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