On 22/01/2012 6:02 PM, Chandan Choudhury wrote:
Hi gmx-users !!
How does the gromacs unfolds the coordinates of the atoms when the
simulation is run using -pbc xyz ?
I do not know what you mean by "unfold".
If a particle in subsequent time crosses the boundary say x / y or
both axis , then the box x/y or both vector(s) is added to obtain a
folded trajectory. While unfolding, an atom, there are two or more
image points, which one to choose. I think minimum image condition can
handle this, but do not know how. Can some of help me out.
You can choose any of the infinite number of equivalent periodic images.
The best one to choose depends what you want to do with them next. See
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Mark
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