[gmx-users] Reverse micelle clustering issue

V.V.Chaban vvchaban at gmail.com
Tue Jul 21 22:39:13 CEST 2015

The general advice to use trjconv  with every keyword independently.

In certain cases, its behavior is fairly bizarre if one uses all
keywords at the same time. Probably, order of called procedures in the
code matters...

Professor Vitaly V. Chaban

On Tue, Jul 21, 2015 at 3:08 PM, Tyler Cropley <tyler.cropley at wagner.edu> wrote:
> Dear Gromacs users,
>  We ran a simulation of an AOT reverse micelle in isooctane solvent. We
> followed instructions
> http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering . For
> clustering we selected the group that contains AOT and for output we
> selected the entire system. The reverse micelle appears outside of the
> solvent box in vmd. This is the picture
> http://s24.photobucket.com/user/tycropley/media/RM-issue_zpsbngarszw.png.html
> . We used -center and -boxcenter for trjconv but it did not work.
>  Is there a way to ensure that the corrected trajectory displays the
> reverse micelle inside the solvent box? Or is there something more
> seriously wrong?
>  Thank you,
> Tyler
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