[gmx-users] ion jumping out of water box

[Mark Abraham]

On 11/01/2011 7:51 AM, Tsjerk Wassenaar wrote:
> 1. First make your molecules whole if you want them whole.
> 2. Cluster your molecules/particles if you want them clustered.
> 3. Extract the first frame from the trajectory as reference for
> removing jumps if you want to remove jumps
> 4. Remove jumps if you want to have them removed using the first frame :p
> 5. Center your system using some criterium (shifts the system, so
> don't use -pbc nojump after this step)
> 6. Put everything in some box
> 7. Fit if desired and don't use any PBC related option afterwards.
>
> Not all steps have to be taken of course.
>
> With point three, the issue is that trjconv removes the jumps from the
> first frame using the reference structure provided with -s. If the
> reference structure (run input file) is not clustered/whole, trjconv
> -pbc nojump will undo steps 1 and 2

I wiki-fied this here 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Mark