[gmx-users] radial distribution function

[Erik Marklund]

I think that Qiao is right, and I also think that it's an easy thing to test on a simple test system consisting of a just a single solute molecule (a single atom to keep it simple) and just a few solvent molecules (a single one is even easier).

/Erik Marklund
  ----- Original Message ----- 
  From: Qiao Baofu 
  To: Discussion list for GROMACS users 
  Sent: Wednesday, November 22, 2006 1:39 PM
  Subject: Re: [gmx-users] radial distribution function


  To my knowledge, g_rdf calculate all the atoms of group A to all the atoms of group B to get the gAB(r). g_rdf -com calculate the center of group A, not the centers of the residues in group A to all the atoms of group B.  

  I upload a file based on gmx_rdf.c to calculate the centers of residues of group A (and B) last month to the website of gromacs. 


  2006/11/22, Nguyen Hoang Phuong < phuong at theochem.uni-frankfurt.de>:

    My question is that how does gromacs compute 
    g(r)? Is r the distance between center of mass
    of the group [ Pep ] and the center of mass of each
    solvent molecule? Or gromacs computes g_i(r) between
    each atom of the group [ Pep] with respect to solvent
    molecules and then take average over all g_i(r) to get
    g(r)?

    Many thanks in advance,

    Phuong
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  Baofu Qiao



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