[gmx-users] Regarding TCoupling and position restraints
hanniballecter13 at gmail.com
Sat Aug 17 06:10:41 CEST 2013
Thanks. Is there any way to position restraint a part of the system while
keeping all bonds flexible?
On Fri, Aug 16, 2013 at 5:24 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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.
> Postdoctoral Fellow
> 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 <jalemkul at outerbanks.umaryland.edu> | (410)
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