[gmx-users] How to use different reference structures for g_covar and g_anaeig

David van der Spoel spoel at xray.bmc.uu.se
Wed May 16 21:46:43 CEST 2007

sridhar at cdfd.org.in wrote:
> Dear All,
> I have two specific questions:
> 1.I have been to do COMBINED ESSENTIAL dynamics by concatenating two
> trajectories. I calcualted the covariance matrix using the default options
> of g_covar. This should presumably use the average structure for fitting.
> Now I want to use one of a different structure other than the average
> structure of the two trajectories in g_anaeig. It was said in the
> gmx-mailing lists that g_anaeig uses the structure in the eigenvec.trr
> file if present, otherwise it takes the structure given in the -s option.
> But I suppose the structure file is always present in the eigenvec.trr
> file. Is there any way that we can ignore the structure file in
> eigenvec.trr file and use the file supplied in -s option of g_anaeig?
the trr file does not contain a structure, but it one can deduce an 
average from it.
> 2. Further, in the case of COMBINED ESSENTIAL DYNAMICS, many researchers
> could compute the Mean square fluctuation by individual trajectories
> projected on to the combined eigenvectors using the covariance matrix. Can
> any one explain how to calculate this?
probably it is done separately as well as combined.

> g_anaeig of COMBINED ESSENTIAL DYNAMICS can give eigenrmsf of only the
> combined trajectory!
that is correct I think.
> Thanks
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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