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<p>Thanks, David.</p>
<p><br></p>
<p>Sorry, maybe my questions were too fuzzy.</p>
<p><br></p>
<p>They concern the definition of cluster in these codes.</p>
<p>1) When we estimate through single linkage whether the structure belongs to the cluster we should find the smallest distance between any element of the structure and any element of cluster, then compare this distance with the cutoff value. I don't understand how this cutoff value may have "root mean square deviation" feature.</p>
<p><br></p>
<p>2) To my knowledge the g_clustsize uses the same "single linkage" algorithm for cluster construction. If so, there should be the similar cut-off parameter. The -cut option looks like this one. But very different default values of these parameters (cutoff=0.1 in g_cluster and cut=0.35 in g_clustsize) are doubted to me. </p>
<p><br></p>
<p>These two questions may be reformulated to single one:</p>
<p>If I would apply these two codes (using single linkage with default values) to the same system how different would be the cluster partitions?</p>
<p><br></p>
<p>Thanks one more.</p>
<p>Dmitri</p>
<p><br></p>
<p><span class=rvts6>> Dmitri Dubov wrote:</span></p>
<p><span class=rvts7>>> Dear gmx'ers,</span></p>
<p><br></p>
<p><br></p>
<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>
<p><br></p>
<p><br></p>
<p><span class=rvts7>>> 1) Manual for g_cluster:</span></p>
<p><br></p>
<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>
<p><br></p>
<p><span class=rvts7>>> Other options...</span></p>
<p><br></p>
<p><span class=rvts7>>> -cutoff real 0.1 RMSD cut-off (nm) for two structures to be neighbor"</span></p>
<p><br></p>
<p><span class=rvts7>>> What does "RMSD" mean here?</span></p>
<p><span class=rvts6>> Root mean square deviation. Typical for proteins.</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts7>>> 2) Manual for g_clustsize:</span></p>
<p><br></p>
<p><span class=rvts7>>> "-cut real 0.35 Largest distance (nm) to be considered in a cluster"</span></p>
<p><br></p>
<p><span class=rvts7>>> Is there any difference between -cut and -cutoff in g_cluster above?</span></p>
<p><br></p>
<p><span class=rvts6>> These are two different programs, unfortunately not sharing any code.</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts7>>> Thanks.</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts7>>> Dmitri</span></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><span class=rvts7>>> ------------------------------------------------------------------------</span></p>
<p><br></p>
<p><span class=rvts7>>> _______________________________________________</span></p>
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