Dear Tsjerk and Ran, I would like to try your modified versions of g_clustsize and trjconv as well since I am facing similar issues on the analyses of micellar systems.
with kind regards, Andre On Thu, Apr 14, 2011 at 5:29 PM, jim jack <[email protected]> wrote: > 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 > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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