Re: [gmx-users] Re: Nose-Hover chains for membrane protein simulation
Michael, thanks for suggestions. the main reason of ussage N-H with chains is the assumption that simple N-H does not provide ergodicity of the system assuming that I'd like to sample all temperature acceptable conformations on the 100 ns trajectory. But as I understood the chain regime does not compatible with the membrane protein simulation due to the artifacts arising with MTTK batostat. James 2013/6/1 Michael Shirts mrshi...@gmail.com I can't think of any instance where nose-hoover chains provides an advantage over nose-hoover in a large system -- all the demonstrations of superiority are in model systems that are not particularly chaotic. As the system gets more chaotic, it matters less. I would go with md, nose-hoover (w/o chains), and Parrinello-Rahman with semiisotropic scaling. On Sat, Jun 1, 2013 at 1:07 AM, James Starlight jmsstarli...@gmail.com wrote: Performing 5ns simulation after 2 ns equilibration in NPT ensemble (MTTK barostat 5ps coupling ) I've observed non-physical behaviour of my system with the constant drift of the protein molecule as the rigid body in the y-z plane Energy Average Err.Est. RMSD Tot-Drift --- Pressure -760.137 --193.776218.059 (bar) From manual I've noticed that MMTK doest not support *semiisotropic scalling. *Doest it means that with the Nose-hover chains and md-vv I should use only weaker coupling during productions runs (I cant use Parinello;s barostat with such options too) Thanks for help James 2013/5/31 James Starlight jmsstarli...@gmail.com Dear Gromacs users! I'd like to perform simulation of the membrane protein in lipid-water system using Nose-Hover with chains. From manual I've found that with such thermostat I should use (1) md-vv integrator (2) MTTK instead of Parinello's batostat and (3) shake instead of LINCS. How doest such options compatible with the simulation of membrane proteins in general ? On what other options should I pay attention during simulation of membrane protein with NH chains ? Thanks for help, James -- 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 -- 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 -- 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] Re: Nose-Hover chains for membrane protein simulation
And I my point was I didn't think that there was going to be a measurable ergodicity difference between NH chains and NH. Given the size of the system, the chaoticness of atomic motions will likely give you configurational sampling indistinguishable from full ergodicity. Most of the errors that are solved by NH chains are for small toy systems. On Sun, Jun 2, 2013 at 2:17 AM, James Starlight jmsstarli...@gmail.com wrote: Michael, thanks for suggestions. the main reason of ussage N-H with chains is the assumption that simple N-H does not provide ergodicity of the system assuming that I'd like to sample all temperature acceptable conformations on the 100 ns trajectory. But as I understood the chain regime does not compatible with the membrane protein simulation due to the artifacts arising with MTTK batostat. James 2013/6/1 Michael Shirts mrshi...@gmail.com I can't think of any instance where nose-hoover chains provides an advantage over nose-hoover in a large system -- all the demonstrations of superiority are in model systems that are not particularly chaotic. As the system gets more chaotic, it matters less. I would go with md, nose-hoover (w/o chains), and Parrinello-Rahman with semiisotropic scaling. On Sat, Jun 1, 2013 at 1:07 AM, James Starlight jmsstarli...@gmail.com wrote: Performing 5ns simulation after 2 ns equilibration in NPT ensemble (MTTK barostat 5ps coupling ) I've observed non-physical behaviour of my system with the constant drift of the protein molecule as the rigid body in the y-z plane Energy Average Err.Est. RMSD Tot-Drift --- Pressure -760.137 --193.776218.059 (bar) From manual I've noticed that MMTK doest not support *semiisotropic scalling. *Doest it means that with the Nose-hover chains and md-vv I should use only weaker coupling during productions runs (I cant use Parinello;s barostat with such options too) Thanks for help James 2013/5/31 James Starlight jmsstarli...@gmail.com Dear Gromacs users! I'd like to perform simulation of the membrane protein in lipid-water system using Nose-Hover with chains. From manual I've found that with such thermostat I should use (1) md-vv integrator (2) MTTK instead of Parinello's batostat and (3) shake instead of LINCS. How doest such options compatible with the simulation of membrane proteins in general ? On what other options should I pay attention during simulation of membrane protein with NH chains ? Thanks for help, James -- 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 -- 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 -- 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 -- 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] Re: Nose-Hover chains for membrane protein simulation
I can't think of any instance where nose-hoover chains provides an advantage over nose-hoover in a large system -- all the demonstrations of superiority are in model systems that are not particularly chaotic. As the system gets more chaotic, it matters less. I would go with md, nose-hoover (w/o chains), and Parrinello-Rahman with semiisotropic scaling. On Sat, Jun 1, 2013 at 1:07 AM, James Starlight jmsstarli...@gmail.com wrote: Performing 5ns simulation after 2 ns equilibration in NPT ensemble (MTTK barostat 5ps coupling ) I've observed non-physical behaviour of my system with the constant drift of the protein molecule as the rigid body in the y-z plane Energy Average Err.Est. RMSD Tot-Drift --- Pressure -760.137 --193.776218.059 (bar) From manual I've noticed that MMTK doest not support *semiisotropic scalling. *Doest it means that with the Nose-hover chains and md-vv I should use only weaker coupling during productions runs (I cant use Parinello;s barostat with such options too) Thanks for help James 2013/5/31 James Starlight jmsstarli...@gmail.com Dear Gromacs users! I'd like to perform simulation of the membrane protein in lipid-water system using Nose-Hover with chains. From manual I've found that with such thermostat I should use (1) md-vv integrator (2) MTTK instead of Parinello's batostat and (3) shake instead of LINCS. How doest such options compatible with the simulation of membrane proteins in general ? On what other options should I pay attention during simulation of membrane protein with NH chains ? Thanks for help, James -- 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 -- 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
[gmx-users] Re: Nose-Hover chains for membrane protein simulation
Performing 5ns simulation after 2 ns equilibration in NPT ensemble (MTTK barostat 5ps coupling ) I've observed non-physical behaviour of my system with the constant drift of the protein molecule as the rigid body in the y-z plane Energy Average Err.Est. RMSD Tot-Drift --- Pressure -760.137 --193.776218.059 (bar) From manual I've noticed that MMTK doest not support *semiisotropic scalling. *Doest it means that with the Nose-hover chains and md-vv I should use only weaker coupling during productions runs (I cant use Parinello;s barostat with such options too) Thanks for help James 2013/5/31 James Starlight jmsstarli...@gmail.com Dear Gromacs users! I'd like to perform simulation of the membrane protein in lipid-water system using Nose-Hover with chains. From manual I've found that with such thermostat I should use (1) md-vv integrator (2) MTTK instead of Parinello's batostat and (3) shake instead of LINCS. How doest such options compatible with the simulation of membrane proteins in general ? On what other options should I pay attention during simulation of membrane protein with NH chains ? Thanks for help, James -- 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
