[gmx-users] Regarding TCoupling and position restraints
jalemkul at vt.edu
Sat Aug 17 12:22:51 CEST 2013
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.
> 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)
>> gmx-users mailing list gmx-users at gromacs.org
>> * 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>
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
More information about the gromacs.org_gmx-users