> Can Amber confine range to calculate mean square displacement? If
> i want to calculate mean square displacement of water in the carbon
> nanotubes not outside ,how should i do?
Since waters can exchange, you might want something more like
population analysis, calculating the density of waters on a grid
within the tube. I believe ptraj can do this.
Ptraj may be able to calculate rms of a group of residues (waters),
but you would have to figure out which ones are in the tube.
Bill
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Received on Tue Oct 13 2009 - 17:30:04 PDT
