[gmx-users] Reverse micelle clustering issue

[Tyler Cropley]

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