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 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
