Now got the point. Thank you Tsjerk Sir and Prof. David for the help.
On Wed, Jul 31, 2013 at 1:42 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi Bipin, > > If A/C have RMSD 0.4 nm, but A/B and B/C both have RMSD < 0.3 nm, they'll > end up in the same cluster. > > Cheers, > > Tsjerk > > > On Wed, Jul 31, 2013 at 9:45 AM, bipin singh <bipinel...@gmail.com> wrote: > > > Thanks for the reply Prof. David. But in the output it shows that "The > RMSD > > ranges from 0.0602553 to 0.411066 nm"; this is the point of confusion to > > me. So I think it should write the snapshots having RMSD greater than > 0.3nm > > (cutoff) to another cluster. > > > > > > On Wed, Jul 31, 2013 at 12:59 PM, David van der Spoel > > <sp...@xray.bmc.uu.se>wrote: > > > > > On 2013-07-31 07:20, bipin singh wrote: > > > > > >> Hello All, > > >> > > >> I was trying to do clustering on my MD trajectory using gromos method > > >> under > > >> g_cluster module. I got one doubt regarding the output, as I used the > > >> cutoff of 0.3nm for RMSD calculation, I was expecting that all the > > >> snapshots which have RMSD less than or equal to 0.3nm will form the > > first > > >> cluster and the rest of snapshots will form another cluster. But the > > >> output > > >> gives a single cluster. Please let me know if I have not understood it > > >> correctly. > > >> > > > > > > It means everything is within 0.3 nm RMSD from each other. Maybe your > > > system is very stable or you did not simulate very long. You can use a > > > shorter cut-off. > > > > > > > > >> I am appending the output below: > > >> > > >> ##############################**###################### > > >> Using gromos method for clustering > > >> Using RMSD cutoff 0.3 nm > > >> The RMSD ranges from 0.0602553 to 0.411066 nm > > >> Average RMSD is 0.107366 > > >> Number of structures for matrix 12501 > > >> Energy of the matrix is 960.075 nm > > >> > > >> Found 1 clusters > > >> > > >> Writing middle structure for each cluster to clusters.pdb > > >> Counted 0 transitions in total, max 0 between two specific clusters > > >> ##############################**######################## > > >> > > >> > > > > > > -- > > > David van der Spoel, Ph.D., Professor of Biology > > > Dept. of Cell & Molec. Biol., Uppsala University. > > > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > > > sp...@xray.bmc.uu.se http://folding.bmc.uu.se > > > -- > > > gmx-users mailing list gmx-users@gromacs.org > > > http://lists.gromacs.org/**mailman/listinfo/gmx-users< > > http://lists.gromacs.org/mailman/listinfo/gmx-users> > > > * Please search the archive at http://www.gromacs.org/** > > > Support/Mailing_Lists/Search< > > 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< > > http://www.gromacs.org/Support/Mailing_Lists> > > > > > > > > > > > -- > > *----------------------- > > Thanks and Regards, > > Bipin Singh* > > -- > > 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 > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > 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 > -- *----------------------- Thanks and Regards, Bipin Singh* -- 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
