[gmx-users] Regarding TCoupling and position restraints

HANNIBAL LECTER 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:
>
>> 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
>
> --
> ==============================**====================
>
> 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)
> 706-7441
>
> ==============================**====================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>



More information about the gromacs.org_gmx-users mailing list