[gmx-users] micelles and trjconv -pbc cluster

jim jack blhawk13 at yahoo.com
Thu Apr 14 16:42:04 CEST 2011

Dear GROMACS users, 

   I am trying to simulate an SDS micelle in water. As simulation time goes by, the micelle approaches the edge of the box and consequently some of these molecules get in from the other side. This leads to incorrect radius of gyration, eccentricity, etc. A solution to this problem is the option trjconv -pbc cluster as described in the page http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering. In this case, the problem is that it takes a lot of time and a huge file (several GB) is created due to this procedure. Is there any other alternative?

Thanks in advance

George Koros

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