Hi Tang,<br><br>It's just the general case of least-squares fitting:<br><br>1. Bring centres of geometry/mass to origin<br>2. Calculate (mass-weighted) rotation matrix<br>3. Rotate structure<br>(4. Calculate squared displacements)
<br><br>But what do you mean with 'very different'. Can you provide an example? What command line did you use? Do you have multiple subunits and have jumps over PBC between the two reference structures?<br><br>Cheers,
<br><br>Tsjerk<br><br><div class="gmail_quote">On Jan 3, 2008 3:37 PM, tangxuan <<a href="mailto:tangxuan82@gmail.com">tangxuan82@gmail.com</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>Does anyone know how fitting step works in detail when running g_rmsf?<br>When I used two different tpr files with same protein structure but<br>different atoms position, the result is very different.<br>Can you explain this ?
<br>many thanks!<br><br>Tang<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">
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</a><br></blockquote></div><br><br clear="all"><br>-- <br>Tsjerk A. Wassenaar, Ph.D.<br>Junior UD (post-doc)<br>Biomolecular NMR, Bijvoet Center<br>Utrecht University<br>Padualaan 8 <br>3584 CH Utrecht<br>The Netherlands<br>
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