[gmx-users] Center of simulation box

[Justin A. Lemkul]

zhenlong li wrote:
> Dear all,
> 
> In my simulation, when the simulation box shrinks, the center of box 
> always shift towards the origin even if the center motion is set to 
> removed every timestep.
> I just wonder if there is an anticipated center position for a given 
> simulation box in gromacs. The box type is dodecahedron in my simulation.
> 

Yes, this is expected.  By default, a unit cell built by Gromacs will be 
centered at (x/2, y/2, z/2).

> My problem is how to make sure a group of atoms, such as proteins,  sit 
> at the center of the simulation box after the simulation box become stable.
> Current, as the center of the box floats, it is very difficult to 
> maintain it by position restraint of the center group.
> 

If you are applying periodic boundary conditions, there is no such thing as a 
center (since the system is infinite).  While it may be a useful convention for 
visualization purposes, there is no effect on the calculation itself.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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