Hi Erik, Thank you very much from your response.
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: Monday, April 16, 2012 12:07 PM Subject: Re: [gmx-users] Clustering 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
