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<html><head><title>Re[2]: [gmx-users] params for g_cluster and g_clustsize</title>
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<p>Hi, Erik!</p>
<p><br></p>
<p>Many thanks for your exhaustive reply.</p>
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<p><span class=rvts6>> Dmitri Dubov skrev:</span></p>
<p><br></p>
<p><span class=rvts7>>> Thanks, David.</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts7>>> Sorry, maybe my questions were too fuzzy.</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts7>>> They concern the definition of cluster in these codes.</span></p>
<p><br></p>
<p><span class=rvts7>>> 1) When we estimate through single linkage whether the structure </span></p>
<p><span class=rvts7>>> belongs to the cluster we should find the smallest distance between </span></p>
<p><span class=rvts7>>> any element of the structure and any element of cluster, then compare </span></p>
<p><span class=rvts7>>> this distance with the cutoff value. I don't understand how this </span></p>
<p><span class=rvts7>>> cutoff value may have "root mean square deviation" feature.</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts6>> The rmsd is given in nm, and if the rmsd falls below the cutoff (also </span></p>
<p><span class=rvts6>> given in nm, of course) the two frames are part of the same cluster when</span></p>
<p><span class=rvts6>> single lincage is used for g_cluster.</span></p>
<p><br></p>
<p><span class=rvts7>>> 2) To my knowledge the g_clustsize uses the same "single linkage" </span></p>
<p><span class=rvts7>>> algorithm for cluster construction. If so, there should be the similar </span></p>
<p><span class=rvts7>>> cut-off parameter. The -cut option looks like this one. But very </span></p>
<p><span class=rvts7>>> different default values of these parameters (cutoff=0.1 in g_cluster </span></p>
<p><span class=rvts7>>> and cut=0.35 in g_clustsize) are doubted to me.</span></p>
<p><br></p>
<p><span class=rvts6>> Here's what I believe you've not quite grasped: g_cluster clusters </span></p>
<p><span class=rvts6>> *frames* in a trajectory, generating groups of structures; g_clustsize</span></p>
<p><span class=rvts6>> clusters atoms/molecules *within each frame*. That said, the low default</span></p>
<p><span class=rvts6>> cutoff for g_cluster makes it less likely that you will end up with all</span></p>
<p><span class=rvts6>> frames in the same cluster, and the higher default cut-off for </span></p>
<p><span class=rvts6>> g_clustsize is the typical hydrogen bond length and is useful for </span></p>
<p><span class=rvts6>> finding water clusters, e.g. droplets in vacuo.</span></p>
<p><br></p>
<p>OK, I was using g_clustsize for similar aim. Not understanding <span class=rvts6>g_cluster action </span>I fell into idle trouble about correctness of my analysis<span class=rvts6>.</span></p>
<p><br></p>
<p><span class=rvts7>>> These two questions may be reformulated to single one:</span></p>
<p><br></p>
<p><span class=rvts7>>> If I would apply these two codes (using single linkage with default </span></p>
<p><span class=rvts7>>> values) to the same system how different would be the cluster partitions?</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts6>> One would be clusters containing frames, the other clusters containing</span></p>
<p><span class=rvts6>> atoms/molecules. They are used for completely different things.</span></p>
<p><br></p>
<p><span class=rvts6>> /Erik</span></p>
<p><br></p>
<p><span class=rvts7>>> Thanks one more.</span></p>
<p><br></p>
<p><span class=rvts7>>> Dmitri</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts7>>> > Dmitri Dubov wrote:</span></p>
<p><br></p>
<p><span class=rvts7>>> >> Dear gmx'ers,</span></p>
<p><br></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><br></p>
<p><span class=rvts7>>> >> g_clustsize programs?</span></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><span class=rvts7>>> >> 1) Manual for g_cluster:</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts7>>> >> "single linkage: add a structure to a cluster when its distance to any </span></p>
<p><br></p>
<p><span class=rvts7>>> >> element of the cluster is less than cutoff...</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts7>>> >> Other options...</span></p>
<p><br></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><br></p>
<p><span class=rvts7>>> >> What does "RMSD" mean here?</span></p>
<p><br></p>
<p><span class=rvts7>>> > Root mean square deviation. Typical for proteins.</span></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><span class=rvts7>>> >> 2) Manual for g_clustsize:</span></p>
<p><br></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><br></p>
<p><span class=rvts7>>> >> Is there any difference between -cut and -cutoff in g_cluster above?</span></p>
<p><br></p>
<p><br></p>
<p><span class=rvts7>>> > These are two different programs, unfortunately not sharing any code.</span></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><span class=rvts7>>> >> Thanks.</span></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><span class=rvts7>>> >> Dmitri</span></p>
<p><br></p>
<p><br></p>
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<p><br></p>
<p><span class=rvts7>>> >> ------------------------------------------------------------------------</span></p>
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<p><br></p>
<p><span class=rvts7>>> >> _______________________________________________</span></p>
<p><br></p>
<p><span class=rvts7>>> >> gmx-users mailing list </span><a class=rvts8 href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><span class=rvts9> </span></p>
<p><span class=rvts7>>> <</span><a class=rvts8 href="mailto:gmx-users@gromacs.org">mailto:gmx-users@gromacs.org</a><span class=rvts9>></span></p>
<p><br></p>
<p><span class=rvts7>>> >> </span><a class=rvts8 href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a></p>
<p><br></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 </span></p>
<p><span class=rvts7>>> posting!</span></p>
<p><br></p>
<p><span class=rvts7>>> >> Please don't post (un)subscribe requests to the list. Use the </span></p>
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<p><span class=rvts7>>> >> www interface or send it to </span><a class=rvts8 href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><span class=rvts9> </span></p>
<p><span class=rvts7>>> <</span><a class=rvts8 href="mailto:gmx-users-request@gromacs.org">mailto:gmx-users-request@gromacs.org</a><span class=rvts9>>.</span></p>
<p><br></p>
<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>
<p><br></p>
<p><br></p>
<p><span class=rvts7>>> ------------------------------------------------------------------------</span></p>
<p><br></p>
<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>
<p><span class=rvts7>>> Please don't post (un)subscribe requests to the list. Use the </span></p>
<p><span class=rvts7>>> www interface or send it to </span><a class=rvts8 href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><span class=rvts9>.</span></p>
<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>
<p><br></p>
<p><br></p>
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<p><br></p>
<p><span class=rvts10>-- </span></p>
<p><span class=rvts10>Regards,</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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