[gmx-users] Periodic Boundary Conditions

Justin Lemkul jalemkul at vt.edu
Mon Feb 11 21:15:01 CET 2019

On 2/10/19 12:26 PM, marzieh gharouni wrote:
> Hello
> I want to do noPeriodic Boundary Conditions for my system.
> Gromacs tutorial has said that it can not be used the center and nojump in
> one command simultaneously.
> I would be grateful if you could explain the reasons for it?

Both apply translations to the coordinates, which are going to be in 
conflict with one another. The use of -pbc nojump allows atoms to appear 
to stray "outside" the box, but then trying to center them will try to 
move them back towards the middle of the box. These are mutually 
exclusive operations.



Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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