[gmx-users] Regarding TCoupling and position restraints
hanniballecter13 at gmail.com
Fri Aug 16 23:09:18 CEST 2013
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
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?
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