[gmx-users] pair-distance distribution function

Daniela S. Mueller d.s.mueller at rug.nl
Sat Feb 4 01:37:27 CET 2006

hi jon,

if you want to calculate the distances between all atom pairs within the 
protein, maybe g_rms or g_rmsdist is more suitable. i think for g_rms 
you need the option '-what rho' (i'm not totally sure).

good luck.

Jon Ellis wrote:
> Daniela, thank you for your help.
> I tried using g_rdf to calculate the vector lengths of all atom-pair 
> distances in a protein. I dumped a single frame from my trajectory using 
> trjconv, then ran
>    g_rdf -f protein.gro -o rdf -n protein.ndx -bin 0.001
> This gave me what appeared to be a pair distance distribution, except 
> that it seemed to truncate the list at r=4.085 nm, and the P(r) value at 
> this r was non-zero. I know from other analyses that the protein should 
> have longer distances than 4 nm. I tried different bin sizes, and 
> different endq and startq values, but the result remained the same.
> Is there something I'm missing, or can I not do pair-distance 
> distribution functions using g_rdf?
> Cheers
> Jon
>> hi jon,
>> g_rdf counts the radial distribution function of an index group around 
>> another index group.
>> daniela
>> Jon wrote:
>>> / Hello
>> />/ />/ Is there a program in Gromacs, or a standalone program, to 
>> calculate the />/  pair-distance distribution function P(r), aka the 
>> vector length />/ distribution, for a protein?
>> />/ />/ The algorithm is P(r)=Dn(r)/nDr, where Dn(r) is the number of 
>> atom pairs />/ whose separation is between r-Dr/2 and r+Dr/2, and n is 
>> the total number />/ of atoms in the system.
>> />/ />/ I would appreciate any help.
>> />/ />/ Cheers
>> />/ Jon
>> />/ /


Daniela S. Mueller

- MD group, RuG -

Molecular Dynamics
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands

Email: d.s.mueller at rug.nl

Website: http://www.rug.nl/gbb/md

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