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
