[gmx-users] how to remove periodicity when using g_rmsd

[Erik Marklund]

My first guess, without knowing how you used g_rms, is that the larde  
rmsd for certain subunits is due to inadequate roto-translational fit  
prior to rmsd-calculation. Does that help? If not, please be more  
explicit about what you aim to do and what you have done.

/Erik

27 sep 2007 kl. 11.29 skrev TANG JIAOWEI:

> Dear all,
> I am studying on a big protein with 16 subunits and when i used  
> g_rmsd to one subunit of the protein, the result seems strange that  
> the structure of the subunit changes much but it should not.. I  
> searched the mailing list and it may be caused by the periodic  
> thing. Could you tell me how to remove the periodic thing in detail  
> before i use g_rmsd.
>
> Thank you
>
> Tang jiaowei
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_______________________________________________
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,	75124 Uppsala, Sweden
phone:	+46 18 471 4537		fax: +46 18 511 755
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys


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