[AMBER] RDF between centers of mass/geometry

From: Lorenzo Gontrani <lorenzo.gontrani.uniroma1.it>
Date: Thu, 12 Jan 2017 11:36:43 +0100

Dear Amber experts, I was wondering if there is a "simple" way of
calculating the radial distribution function between the centers of
mass/geometry of two residues RES1 and RES2 of a given mixture.

I am using the command

radial <rdf.dat> 0.02 23 :RES1 :RES2.C1 volume center1

I found that atom C1 is close to RES1 center and can do something
similar for RES2.

I remember that ptraj had sofisticated capabilities for calculating
vectors between mass centers..could I use something of that kind?

Another question: what about dumping the trajectory of these centers of

Thanks for any advice


      Lorenzo Gontrani
      Research associate - EDXD group
      University of Rome "La Sapienza"
      ResearcherID: L-6061-2014
      GSM +39 338 7615798
      Email lorenzo DOT gontrani AT uniroma1 DOT it
      Webpage: http://webcaminiti/gontrani.html
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Received on Thu Jan 12 2017 - 03:00:02 PST
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