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.
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