Dear Ran Friedman and Tsjerk Wassennaar, First of all, thanks to all responses to my problem. As far as the modified versions of g_clustsize and trjconv, I really want to try them. Best regards
George Koros --- On Thu, 4/14/11, jim jack <[email protected]> wrote: From: jim jack <[email protected]> Subject: micelles and trjconv -pbc cluster To: [email protected] Date: Thursday, April 14, 2011, 7:42 AM 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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