[gmx-users] Regarding TCoupling and position restraints
jalemkul at vt.edu
Fri Aug 16 23:24:56 CEST 2013
On 8/16/13 5:09 PM, HANNIBAL LECTER wrote:
> 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?
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 A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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