[gmx-users] rdf

David van der Spoel spoel at xray.bmc.uu.se
Wed Nov 1 09:49:19 CET 2006

On Tue, 31 Oct 2006, Claus Valka wrote:

>Title : radial distribution function, 31.10.06
>      Hello, 
>      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
>      for   
>      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?

You will have to make an elaborate index file, covering e.g. C in chain 2, 
C in chain 3 and so on, compute all the rdfs and then avreage afterwards. 
Note that averaging depends on the normalization. If all your chains are 
identical you can do this by linear averaging.

A further option to get only intermolecular RDFs is by making an extra tpr 
file, especially for thisss purpose where you increase the number of 
exclusions to a number such that all intramolecular interactions are 
excluded., for e.g. united-atom decane the number of exclusions would have 
to be nine. Don't use this tpr for simulations though!

>      Any help would be appreciated,
>      Nick
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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