Hi George, Recently I wrote an alternative, non-iterative clustering routine, that does not suffer from convergence failures. If you want, I can send you the modified trjconv source code. Note that it does not bother about the center of mass of the cluster, but just builds a network of neighbours, until there are no more. If you're clusters are not periodic, it won't matter.
Let me know... Cheers, Tsjerk On Thu, Apr 14, 2011 at 4:48 PM, Erik Marklund <[email protected]> wrote: > jim jack skrev 2011-04-14 16.42: > > 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 > > I don't think that the cluster option always converges. You could, if > your micelle is intact at frame 0, first do trjconv -pbc nojump, then > optionally trjconv -center. That should give a trajectory from which you > could calculate the radius of gyration. If SDS molecules occationally leave > the micelle and recombine with a priodic, then you might have a problem with > the suggested approach. > > -- > ----------------------------------------------- > Erik Marklund, PhD student > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 4537 fax: +46 18 511 [email protected] > http://folding.bmc.uu.se/ > > > -- > 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 > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands
-- 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
