<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Dear all,<br>for my cluster analysis I am using the g_cluster tool with the gromos method.<br>The problem is that I have to compare the results for system of different lengths, and of course the result of the cluster analysis changes according to the cutoff chosen. So what will be a great choice in this case?<br>I was thinking about different possibilities, namely: i) choosing - as it is quite frequent in the literature - an arbitrary cutoff (like the default 0.1), but using the same for different systems would be probably not suitable...<br>ii) looking for every case at the RMSD distribution and choosing the minimum value between the two peaks - in this case the cutoff would vary for every system; iii) choosing for every system the cutoff that allows to have in the largest cluster the 50% of the structures, and also in this case the cutoff would be different for the different cases...<br><br>Any hint?<br>Thanks a lot,<br>Valeria</div><div><br></div><div><br></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Valeria Losasso</div><div><a href="mailto:v.losasso@grs-sim.de">v.losasso@grs-sim.de</a></div><div><br></div><div>German Research School for<br>Simulation Sciences GmbH<br>52425 Jülich | Germany<br><br>Tel +49 2461 61 8934<br>Web <a href="http://www.grs-sim.de/">www.grs-sim.de</a><br><br>Members: Forschungszentrum Jülich GmbH | RWTH Aachen University<br>Registered in the commercial register of the local court of<br>Düren (Amtsgericht Düren) under registration number HRB 5268<br>Registered office: Jülich<br>Executive board: Prof. Marek Behr Ph.D. | Dr. Norbert Drewes</div><div><br></div><div><br></div><div><br></div></div></span><br class="Apple-interchange-newline"></div><br class="Apple-interchange-newline"></div></div></span><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline">
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