On Sun, Oct 08, 2006, Rita Cassia wrote:
>
> I had taken a look with VMD how those structures look like and I had seen
> that 2 Pheophorbides were crossing each other.
>
> Unfortunately, when I used NAMD to start my simulation with 0° K, NAMD
> stopped the simulation, saying that a certain atom was moving too fast and
> as consequence other atoms too...
You could try a minimization first, rather than MD. That might help fix up
a bad initial structure. However, if the "crossing" is quite bad, this might
not help either.
....good luck...dac
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Received on Wed Oct 11 2006 - 06:07:06 PDT
