[gmx-users] Reverse micelle clustering issue

Tyler Cropley tyler.cropley at wagner.edu
Tue Jul 21 20:08:57 CEST 2015

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
. 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,


More information about the gromacs.org_gmx-users mailing list