[gmx-users] rdf

Claus Valka lastexile7gr at yahoo.de
Tue Oct 31 13:16:27 CET 2006

Title : radial distribution function, 31.10.06

      I am a new user of Gromacs (just started my
Phd), and
      I'm trying to calculate the partial radial
distibution functions 
      for a system of polymer chains.
      In the topology file the system is described as 
      1)  2 different types of chains 
          (essentially similar in chemistry, with
different helicity)
      2)  C, H, CH3 atom types in each chain (3
different bead types)
      I would like to calculate the rdfs for the
partial correlations
      corresponding to pairs of the type
      a) C   - all   
      b) C   - C
      c) C   - CH3
      d) C   - H
      e) CH3 - H
      A) intra-pairs (same chain)  
      B) inter-pairs (different chains)
      C) any pair
      i.e., pair correlations A[a,b,c,d,e], B[...] and
so on,
      over all chains in the system. 
      In the manual it is said that an index file is
      How could I describe the groups in index file so
as to make these
      calculations in an efficient way? Is there any
easy way to describe
      various kind of desired 'pairing correlations'
in Gromacs?
      Any help would be appreciated,

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