[gmx-users] Re: micelles and trjconv -pbc cluster

[André Farias de Moura]

Dear Tsjerk and Ran,

I would like to try your modified versions of g_clustsize and trjconv as
well
since I am facing similar issues on the analyses of micellar systems.

with kind regards,

Andre

On Thu, Apr 14, 2011 at 5:29 PM, jim jack <blhawk13 at yahoo.com> wrote:

> Dear Ran Friedman and Tsjerk Wassennaar,
>
>
>    First of all, thanks to all responses to my problem. As far as the
> modified versions of g_clustsize and trjconv, I really want to try them.
>
>
>
> Best regards
>
>
> George Koros
>
> --- On *Thu, 4/14/11, jim jack <blhawk13 at yahoo.com>* wrote:
>
>
> From: jim jack <blhawk13 at yahoo.com>
> Subject: micelles and trjconv -pbc cluster
> To: gmx-users at gromacs.org
> Date: Thursday, April 14, 2011, 7:42 AM
>
>
> 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
>
>
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