[gmx-users] Re: micelles and trjconv -pbc cluster

jim jack blhawk13 at yahoo.com
Thu Apr 14 22:29:42 CEST 2011

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 <blhawk13 at yahoo.com> wrote:

From: jim jack <blhawk13 at yahoo.com>
Subject: micelles and trjconv -pbc cluster
To: gmx-users at gromacs.org
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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