Hi, 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.
trjconv -cluster doesn't calculate the sizes or report anything new, so I find it mostly useful for visualization in this context. Best, Erik 15 apr 2012 kl. 12.02 skrev dina dusti: > Dear Erik, > > 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? > > Best Regards > Dina > > From: Erik Marklund <er...@xray.bmc.uu.se> > To: dina dusti <dinadu...@yahoo.com>; Discussion list for GROMACS users > <gmx-users@gromacs.org> > Sent: Sunday, April 15, 2012 12:58 PM > Subject: Re: [gmx-users] Clustering > > Try g_clustsize > > Erik > > 15 apr 2012 kl. 09.00 skrev dina dusti: > >> Dear GROMACS Specialists, >> >> May I know about clustering, Please? >> I want cluster small organic molecules. Is it possible? They collected in >> some places together and they are separate in the other place. >> Please help me. >> >> Thank you very much in advance. >> Best Regards >> Dina >> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > ----------------------------------------------- > Erik Marklund, PhD > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 6688 fax: +46 18 511 755 > er...@xray.bmc.uu.se > http://www2.icm.uu.se/molbio/elflab/index.html > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists ----------------------------------------------- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
