[AMBER] RDF 3 files and 3 columns

From: Philippe Pinard <pp_amber17.yahoo.com>
Date: Mon, 26 Jul 2010 15:19:33 -0700 (PDT)

Dear Amber users

I am interested in computing the radial density distribution of my
I used ptraj for this. I have got 3 .xmgr files generated: volume, standard and
I looked up in the manual amber9, and in the mailing list but I cannot find the
meaning of the 3 columns in each file. I am interested in plotting the radial
density distribution of water HOH inside my macromolecule versus R.
I want to use the center of mass of the macromolecule as the reference. I
performed explicit solvent MD.
My input looks like this:

trajin pdb_bond_wat_md1_exp.mdcrd
trajin pdb_bond_wat_md2_exp.mdcrd
center :1-121 mass origin
image origin center familiar
radial pdb_bond_wat_rad_dens.rdf 0.5 40.0 :HOH_at_O:1-121 closest

I want to do this averaged over 200 ps.

Any help or comments on this are very welcome


AMBER mailing list
Received on Mon Jul 26 2010 - 15:30:03 PDT
Custom Search