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<p>RF> In this case, you topology is read from the .tpr file and all of the molecules there are taken into account for clustering.</p>
<p><br></p>
<p>I think you are right but the following text from the g_clustsize help message has confused me:</p>
<p><br></p>
<p>"</p>
<p>When the -mol option is given clusters will be made out of molecules rather</p>
<p>than atoms, which allows clustering of large molecules. In this case an index</p>
<p>file would still contain atom numbers or your calculcation will die with a</p>
<p>SEGV.</p>
<p>"</p>
<p><br></p>
<p>So what is the sense to make index.ndx if ALL molecules are used for the calculation always...</p>
<p><br></p>
<p><br></p>
<p>Vitaly</p>
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