[gmx-users] Regarding TCoupling and position restraints

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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