[gmx-users] micelles and trjconv -pbc cluster

Mark Abraham Mark.Abraham at anu.edu.au
Thu Apr 14 18:17:19 CEST 2011

On 15/04/2011 12:42 AM, jim jack wrote:
> 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?

Use fewer frames of your trajectory.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110415/1d76e3f3/attachment.html>

More information about the gromacs.org_gmx-users mailing list