[gmx-users] Regarding TCoupling and position restraints

[Justin Lemkul]

On 8/17/13 12:10 AM, HANNIBAL LECTER wrote:
> Thanks. Is there any way to position restraint a part of the system while
> keeping all bonds flexible?
>

Sure.  Apply position restraints as normal and set "constraints = none" in the 
.mdp file.  This will affect your choice of dt, though, and SETTLE is still 
applied to water molecules.

-Justin

>
> 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
>>
>> ==============================**====================
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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
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

==================================================