Re: [gmx-users] Regarding gromos method in g_cluster
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.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-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
Re: [gmx-users] Regarding gromos method in g_cluster
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.sewrote: 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.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- *--- Thanks and Regards, Bipin Singh* -- gmx-users mailing listgmx-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
Re: [gmx-users] Regarding gromos method in g_cluster
On 2013-07-31 09:45, bipin singh 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. I see, then maybe the definition is different (check the source code!). It could be that it is 0.3 nm from the cluster center. On Wed, Jul 31, 2013 at 12:59 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: 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.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-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
Re: [gmx-users] Regarding gromos method in g_cluster
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.sewrote: 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.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-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/Searchbefore 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 listgmx-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 listgmx-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
Re: [gmx-users] Regarding gromos method in g_cluster
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.sewrote: 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.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-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/Searchbefore 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 listgmx-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 listgmx-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 listgmx-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
