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 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> > -- 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
