[gmx-users] micelles and trjconv -pbc cluster

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Apr 14 17:44:07 CEST 2011

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...



On Thu, Apr 14, 2011 at 4:48 PM, Erik Marklund <erikm at xray.bmc.uu.se> 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 755erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/
> --
> gmx-users mailing list    gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110414/2adc27d7/attachment.html>

More information about the gromacs.org_gmx-users mailing list