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
--
========================================
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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