[gmx-users] ion jumping out of water box

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Jan 10 21:51:06 CET 2011

Hey :)

> Unfortunately,
> trjconv takes a bit of experimenting to get working properly, and there is
> no clear how-to to treat the periodicity of any one system.

Sure there is! Just a matter of understanding what you want and
obeying the order:

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

Not really an  answer to the original post, but maybe useful...



> -Justin
>> Thanks,
>> Gidoen
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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