<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Hi Erik,</span></div><div><br><span></span></div><div><span>Thank you very much from your response.</span></div><div><br><span></span></div><div><span>Best Regards</span></div><div><span>Dina</span></div><div><br></div> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font size="2" face="Arial"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Erik Marklund <erikm@xray.bmc.uu.se><br> <b><span style="font-weight: bold;">To:</span></b> dina dusti <dinadusti@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Monday, April 16, 2012 12:07 PM<br> <b><span style="font-weight:
bold;">Subject:</span></b> Re: [gmx-users] Clustering<br> </font> </div> <br>
<meta http-equiv="x-dns-prefetch-control" content="off"><div id="yiv132067666"><div><div>Hi,</div><div><br></div><div>It's been a while since I used g_clustsize, but if I'm not mistaken you get the number of molecules per cluster as output, from which you can estimate the physical size of the clusters with a few assumptions. If that's not good enough you also get the identities of the molecules in the clusters, which you can then use as input, along with the trajectory, for g_gyrate (or similar) to get more information.</div><div><br></div><div>trjconv -cluster doesn't calculate the sizes or report anything new, so I find it mostly useful for visualization in this context.</div><div><br></div><div>Best,</div><div><br></div><div>Erik</div><div><br></div><br><div><div>15 apr 2012 kl. 12.02 skrev dina dusti:</div><br class="yiv132067666Apple-interchange-newline"><blockquote type="cite"><div><div style="color:rgb(0, 0, 0);background-color:rgb(255, 255,
255);font-family:times, serif;font-size:12pt;"><div><span>Dear Erik,</span></div><div><br><span></span></div><div><span>Thank you very much from your response, but I want to calculate the radius of these cluster. I want to know that I should do clustering with trjconv -cluster similar with micelle clustering and then calculate the radius of these?</span></div><div><br><span></span></div><div><span>Best Regards</span></div><div><span>Dina</span></div><div><br></div> <div style="font-family:times new roman, new york, times, serif;font-size:12pt;"> <div style="font-family:times new roman, new york, times, serif;font-size:12pt;"> <div dir="ltr"> <font size="2" face="Arial"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> Erik Marklund <<a rel="nofollow" ymailto="mailto:erikm@xray.bmc.uu.se" target="_blank" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>><br> <b><span style="font-weight:bold;">To:</span></b> dina dusti
<<a rel="nofollow" ymailto="mailto:dinadusti@yahoo.com" target="_blank" href="mailto:dinadusti@yahoo.com">dinadusti@yahoo.com</a>>; Discussion list for GROMACS users <<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>> <br> <b><span style="font-weight:bold;">Sent:</span></b> Sunday, April 15, 2012 12:58 PM<br> <b><span style="font-weight:bold;">Subject:</span></b> Re: [gmx-users] Clustering<br> </font> </div> <br>
<div id="yiv132067666"><div>Try g_clustsize<div><br></div><div>Erik</div><div><br><div><div>15 apr 2012 kl. 09.00 skrev dina dusti:</div><br class="yiv132067666Apple-interchange-newline"><blockquote type="cite"><div><div style="color:#000;background-color:#fff;font-family:times new roman, new york, times, serif;font-size:12pt;"><div>Dear GROMACS Specialists,</div><div><br></div><div>May I know about clustering, Please?</div><div>I want cluster small organic molecules. Is it possible? They collected in some places together and they are separate in the other place.</div><div>Please help me.</div><div><br></div><div>Thank you very much in advance.</div><div>Best Regards</div><div>Dina<br></div><div><br></div><div><br></div></div></div>-- <br>gmx-users mailing list <a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>http://lists.gromacs.org/mailman/listinfo/gmx-users<br>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists</blockquote></div><br><div>
<span class="yiv132067666Apple-style-span" style="border-collapse:separate;color:rgb(0, 0, 0);font-family:Helvetica;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;font-size:medium;"><span class="yiv132067666Apple-style-span" style="border-collapse:separate;color:rgb(0, 0, 0);font-family:Helvetica;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;font-size:medium;"><div style="word-wrap:break-word;"><span class="yiv132067666Apple-style-span" style="border-collapse:separate;color:rgb(0, 0,
0);font-family:Helvetica;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;font-size:medium;"><div style="word-wrap:break-word;"><div>-----------------------------------------------</div><div>Erik Marklund, PhD</div><div>Dept. of Cell and Molecular Biology, Uppsala University.</div><div>Husargatan 3, Box 596, 75124 Uppsala, Sweden</div><div>phone: +46 18 471 6688 fax: +46 18 511 755</div><div><a rel="nofollow" ymailto="mailto:erikm@xray.bmc.uu.se" target="_blank" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a></div><div>http://www2.icm.uu.se/molbio/elflab/index.html</div></div></span></div></span></span>
</div>
<br></div></div></div><br><br> </div> </div> </div></div>-- <br>gmx-users mailing list <a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a rel="nofollow" target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists</blockquote></div><br><div>
<span class="yiv132067666Apple-style-span" style="border-collapse:separate;color:rgb(0, 0, 0);font-family:Helvetica;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;font-size:medium;"><span class="yiv132067666Apple-style-span" style="border-collapse:separate;color:rgb(0, 0, 0);font-family:Helvetica;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;font-size:medium;"><div style="word-wrap:break-word;"><span class="yiv132067666Apple-style-span" style="border-collapse:separate;color:rgb(0, 0,
0);font-family:Helvetica;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;font-size:medium;"><div style="word-wrap:break-word;"><div>-----------------------------------------------</div><div>Erik Marklund, PhD</div><div>Dept. of Cell and Molecular Biology, Uppsala University.</div><div>Husargatan 3, Box 596, 75124 Uppsala, Sweden</div><div>phone: +46 18 471 6688 fax: +46 18 511 755</div><div><a rel="nofollow" ymailto="mailto:erikm@xray.bmc.uu.se" target="_blank" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a></div><div><a rel="nofollow" target="_blank" href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a></div></div></span></div></span></span>
</div>
<br></div></div><meta http-equiv="x-dns-prefetch-control" content="on"><br><br> </div> </div> </div></body></html>