Re: [gmx-users] Regarding TCoupling and position restraints
On 8/17/13 12:10 AM, HANNIBAL LECTER wrote: Thanks. Is there any way to position restraint a part of the system while keeping all bonds flexible? Sure. Apply position restraints as normal and set constraints = none in the .mdp file. This will affect your choice of dt, though, and SETTLE is still applied to water molecules. -Justin On Fri, Aug 16, 2013 at 5:24 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/16/13 5:09 PM, HANNIBAL LECTER wrote: Hi, I am trying to simulate nanotube (1156) with protein and water and I am using Tcoupl = system using sd integrator in gromacs. Since I am position restraining the nanotube, I would expect that the restrained CNT degrees of freedom are accounted for while calculating the system temperatures using g_traj. However, for a ref-t = 300K the system temperature is reported to be ~292K. As a control, I performed simulations with Tcoupl=CNT Protein SOL and in that case the temperatures from g_energy are reported thus CNT~157K Protein~296K and Solvent ~300K. It clearly shows that the CNT constrained dof are not accounted for correctly. Is that the case or am I missing something? Constraints are restraints are different. If you are using constraints on any bonds in your system, the value from g_traj is wrong and you have to manually correct for it. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- 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 -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Regarding TCoupling and position restraints
Hi, I am trying to simulate nanotube (1156) with protein and water and I am using Tcoupl = system using sd integrator in gromacs. Since I am position restraining the nanotube, I would expect that the restrained CNT degrees of freedom are accounted for while calculating the system temperatures using g_traj. However, for a ref-t = 300K the system temperature is reported to be ~292K. As a control, I performed simulations with Tcoupl=CNT Protein SOL and in that case the temperatures from g_energy are reported thus CNT~157K Protein~296K and Solvent ~300K. It clearly shows that the CNT constrained dof are not accounted for correctly. Is that the case or am I missing something? -- 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 TCoupling and position restraints
On 8/16/13 5:09 PM, HANNIBAL LECTER wrote: Hi, I am trying to simulate nanotube (1156) with protein and water and I am using Tcoupl = system using sd integrator in gromacs. Since I am position restraining the nanotube, I would expect that the restrained CNT degrees of freedom are accounted for while calculating the system temperatures using g_traj. However, for a ref-t = 300K the system temperature is reported to be ~292K. As a control, I performed simulations with Tcoupl=CNT Protein SOL and in that case the temperatures from g_energy are reported thus CNT~157K Protein~296K and Solvent ~300K. It clearly shows that the CNT constrained dof are not accounted for correctly. Is that the case or am I missing something? Constraints are restraints are different. If you are using constraints on any bonds in your system, the value from g_traj is wrong and you have to manually correct for it. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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 TCoupling and position restraints
Thanks. Is there any way to position restraint a part of the system while keeping all bonds flexible? On Fri, Aug 16, 2013 at 5:24 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/16/13 5:09 PM, HANNIBAL LECTER wrote: Hi, I am trying to simulate nanotube (1156) with protein and water and I am using Tcoupl = system using sd integrator in gromacs. Since I am position restraining the nanotube, I would expect that the restrained CNT degrees of freedom are accounted for while calculating the system temperatures using g_traj. However, for a ref-t = 300K the system temperature is reported to be ~292K. As a control, I performed simulations with Tcoupl=CNT Protein SOL and in that case the temperatures from g_energy are reported thus CNT~157K Protein~296K and Solvent ~300K. It clearly shows that the CNT constrained dof are not accounted for correctly. Is that the case or am I missing something? Constraints are restraints are different. If you are using constraints on any bonds in your system, the value from g_traj is wrong and you have to manually correct for it. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- 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 -- 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
