[gmx-users] Regarding TCoupling and position restraints

[HANNIBAL LECTER]

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?