[gmx-users] micelles and trjconv -pbc cluster
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://>. 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.
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