<html><body><div style="color:#000; background-color:#fff; font-family:verdana, helvetica, sans-serif;font-size:12pt"><div><span>Dear Prof. Spoel</span></div><div><br><span></span></div><div><span>Thanks for your reply. <br></span></div><div><span>I used g_clustsize and after it, I used g_rdf but it is not true, because the plot of g(r) for tails of surfactants relative to COM of micelle starts from 0 but it is not true!</span></div><div><br></div><div>Best Regards</div><div>Sara<br><span></span></div><div><br></div> <div style="font-family: verdana, helvetica, sans-serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <font face="Arial" size="2"> <hr size="1"> <b><span style="font-weight:bold;">From:</span></b> David van der Spoel <spoel@xray.bmc.uu.se><br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span
style="font-weight: bold;">Sent:</span></b> Sunday, November 27, 2011 3:08 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] g_rdf -com<br> </font> <br>
On 2011-11-27 12:27, mohammad agha wrote:<br>> Dear Prof.<br>><br>> I have a question about g_rdf.<br>> I have a box consists of 500 surfactants that make 10 micelle. I want to<br>> compute rdf for surfactant relative to the center of mass of micelle.<br>> When I do g_rdf, the program ask me 2 groups that the first one is COM,<br>> but it is COM of molecules that I defined in index file.<br>> If I select the surfactant molecules as the first group for COM, this<br>> means the COM of micelle or just surfactants?<br>> If it select just COM of surfactants, then what do I do for selection of<br>> COM of micelle?<br>> Please help me.<br>><br>> Best Regards<br>> Sara<br>><br>><br>you first have to define which surfactants belong together before g_rdf <br>can do this - make an appropriate index file, maybe g_clustsize can help.<br><br>-- <br>David van der Spoel, Ph.D., Professor of Biology<br>Dept. of Cell
& Molec. Biol., Uppsala University.<br>Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br><a ymailto="mailto:spoel@xray.bmc.uu.se" href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> http://folding.bmc.uu.se<br>-- <br>gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" 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 <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br><br><br> </div> </div> </div></body></html>