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<p>Dear gmx'ers,</p>
<p><br></p>
<p>Could you explain me the following points in manuals for g_cluster and g_clustsize programs?</p>
<p><br></p>
<p>1) Manual for g_cluster:</p>
<p>"single linkage: add a structure to a cluster when its distance to any element of the cluster is less than cutoff...</p>
<p>Other options...</p>
<p>-cutoff real 0.1 RMSD cut-off (nm) for two structures to be neighbor"</p>
<p>What does "RMSD" mean here?</p>
<p><br></p>
<p>2) Manual for g_clustsize:</p>
<p>"-cut real 0.35 Largest distance (nm) to be considered in a cluster"</p>
<p>Is there any difference between -cut and -cutoff in g_cluster above?</p>
<p><br></p>
<p>Thanks.</p>
<p><br></p>
<p>Dmitri</p>
<p><span class=rvts6><br></span></p>
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