[gmx-users] micelles and trjconv -pbc cluster

Erik Marklund erikm at xray.bmc.uu.se
Thu Apr 14 16:48:24 CEST 2011

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 
> <http://>. 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 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110414/cdac3ca2/attachment.html>

More information about the gromacs.org_gmx-users mailing list