Re: [gmx-users] Block averaging
On 6/24/16 6:23 AM, sun wrote: Sir If I do averaging of no. of clusters in case of protein (increased no. of clusters as compared to pro-lig complex) at regular intervals of time, It will be sufficient to assess if my simulation is converged? In my case clustering in addition to secondary structure are conclusive parameters. Whatever is physically/biologically meaningful for your system. -Justin Sent from my iPhone On 22-Jun-2016, at 7:09 pm, Justin Lemkulwrote: On 6/22/16 5:02 AM, sun wrote: Hello users and experts I have completed a 200 ns protein ligand simulation using GROMOS 43a1 and Gromacs v 5.0. I expected to observe a conformational change in protein in the presence of ligand and the results are as expected and correlates to previous references as well. So, shall i believe that simulation is converged or there is need to do block averaging over time intervals? If block averaging is required, the parameters like RMSD and propensities for secondary structure are sufficient to conclude that simulation is converged? Or could anyone please tell me a suitable procedure for making blocks and how to average those. With Regards Suniba Just because a simulation produces expected results does not mean it is converged. You must show that any quantities of interest from which you draw your conclusions, are not systematically varying with time. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Block averaging
Sir If I do averaging of no. of clusters in case of protein (increased no. of clusters as compared to pro-lig complex) at regular intervals of time, It will be sufficient to assess if my simulation is converged? In my case clustering in addition to secondary structure are conclusive parameters. Sent from my iPhone > On 22-Jun-2016, at 7:09 pm, Justin Lemkulwrote: > > > >> On 6/22/16 5:02 AM, sun wrote: >> Hello users and experts I have completed a 200 ns protein ligand simulation >> using GROMOS 43a1 and Gromacs v 5.0. I expected to observe a conformational >> change in protein in the presence of ligand and the results are as expected >> and correlates to previous references as well. So, shall i believe that >> simulation is converged or there is need to do block averaging over time >> intervals? If block averaging is required, the parameters like RMSD and >> propensities for secondary structure are sufficient to conclude that >> simulation is converged? Or could anyone please tell me a suitable procedure >> for making blocks and how to average those. With Regards Suniba > > Just because a simulation produces expected results does not mean it is > converged. You must show that any quantities of interest from which you draw > your conclusions, are not systematically varying with time. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Block averaging
Allright Sir Thank you Sent from my iPhone > On 22-Jun-2016, at 7:09 pm, Justin Lemkulwrote: > > > >> On 6/22/16 5:02 AM, sun wrote: >> Hello users and experts I have completed a 200 ns protein ligand simulation >> using GROMOS 43a1 and Gromacs v 5.0. I expected to observe a conformational >> change in protein in the presence of ligand and the results are as expected >> and correlates to previous references as well. So, shall i believe that >> simulation is converged or there is need to do block averaging over time >> intervals? If block averaging is required, the parameters like RMSD and >> propensities for secondary structure are sufficient to conclude that >> simulation is converged? Or could anyone please tell me a suitable procedure >> for making blocks and how to average those. With Regards Suniba > > Just because a simulation produces expected results does not mean it is > converged. You must show that any quantities of interest from which you draw > your conclusions, are not systematically varying with time. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Block averaging
On 6/22/16 5:02 AM, sun wrote: Hello users and experts I have completed a 200 ns protein ligand simulation using GROMOS 43a1 and Gromacs v 5.0. I expected to observe a conformational change in protein in the presence of ligand and the results are as expected and correlates to previous references as well. So, shall i believe that simulation is converged or there is need to do block averaging over time intervals? If block averaging is required, the parameters like RMSD and propensities for secondary structure are sufficient to conclude that simulation is converged? Or could anyone please tell me a suitable procedure for making blocks and how to average those. With Regards Suniba Just because a simulation produces expected results does not mean it is converged. You must show that any quantities of interest from which you draw your conclusions, are not systematically varying with time. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Block averaging
Hello users and experts I have completed a 200 ns protein ligand simulation using GROMOS 43a1 and Gromacs v 5.0. I expected to observe a conformational change in protein in the presence of ligand and the results are as expected and correlates to previous references as well. So, shall i believe that simulation is converged or there is need to do block averaging over time intervals? If block averaging is required, the parameters like RMSD and propensities for secondary structure are sufficient to conclude that simulation is converged? Or could anyone please tell me a suitable procedure for making blocks and how to average those. With Regards Suniba Sent from my iPhone -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.