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<p>In addition to previous letter (Monday is hard-day!)</p>
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<p>It looks like I have known the answers to my questions.</p>
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<p>Maybe the reason is that the g_cluster code compared to g_clustsize includes not only single linkage but also other algorithms. So the RMSD feature and smaller default value of -cutoff (which is unusual for single linkage) relate to other algorithms for cluster partitioning. Is it right?</p>
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<p>Dmitri</p>
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<p><span class=rvts6>> Dmitri Dubov wrote:</span></p>
<p><span class=rvts7>>> Dear gmx'ers,</span></p>
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<p><span class=rvts7>>> Could you explain me the following points in manuals for g_cluster and </span></p>
<p><span class=rvts7>>> g_clustsize programs?</span></p>
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<p><span class=rvts7>>> 1) Manual for g_cluster:</span></p>
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<p><span class=rvts7>>> "single linkage: add a structure to a cluster when its distance to any </span></p>
<p><span class=rvts7>>> element of the cluster is less than cutoff...</span></p>
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<p><span class=rvts7>>> Other options...</span></p>
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<p><span class=rvts7>>> -cutoff real 0.1 RMSD cut-off (nm) for two structures to be neighbor"</span></p>
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<p><span class=rvts7>>> What does "RMSD" mean here?</span></p>
<p><span class=rvts6>> Root mean square deviation. Typical for proteins.</span></p>
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<p><span class=rvts7>>> 2) Manual for g_clustsize:</span></p>
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<p><span class=rvts7>>> "-cut real 0.35 Largest distance (nm) to be considered in a cluster"</span></p>
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<p><span class=rvts7>>> Is there any difference between -cut and -cutoff in g_cluster above?</span></p>
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<p><span class=rvts6>> These are two different programs, unfortunately not sharing any code.</span></p>
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<p><span class=rvts7>>> Thanks.</span></p>
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<p><span class=rvts7>>> Dmitri</span></p>
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<p><span class=rvts7>>> ------------------------------------------------------------------------</span></p>
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<p><span class=rvts7>>> _______________________________________________</span></p>
<p><span class=rvts7>>> gmx-users mailing list </span><a class=rvts8 href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a></p>
<p><a class=rvts8 href="http://lists.gromacs.org/mailman/listinfo/gmx-users">>> http://lists.gromacs.org/mailman/listinfo/gmx-users</a></p>
<p><span class=rvts7>>> Please search the archive at </span><a class=rvts8 href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><span class=rvts9> before posting!</span></p>
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<p><span class=rvts7>>> Can't post? Read </span><a class=rvts8 href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a></p>
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<p><span class=rvts10>-- </span></p>
<p><span class=rvts10>С уважением,</span></p>
<p><span class=rvts10> Dmitri </span><a class=rvts11 href="mailto:ddubov@ngs.ru">mailto:ddubov@ngs.ru</a></p>
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