AMBER Archive (2009)

Subject: Re: [AMBER] mean square displacment

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Oct 13 2009 - 19:09:49 CDT

> 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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