[gmx-users] g_cluster, RMSD distribution

Ran Friedman r.friedman at bioc.uzh.ch
Wed May 19 16:47:49 CEST 2010


The distribution is calculated as follows:
101 bins are formed between zero and maximum rmsd in equal separation
(by calculating the largest value by 100 to create the separation). Each
rmsd value is put into the right bin and the counter for that bin is
increased by 1. The total number of counts is the size of half a matrix.

If the maximal rmsd is 10.0 and a certain comparison yield rmsd=0.13 the
value of the second bin in increased by 1.


Michał Koliński wrote:
> Dear All
> I’m trying to obtain RMSD distribution of  a ligand in the binding site of the receptor protein during 40 ns MD simulation.
> Could you please explain:
> - what is exactly the yaxis unit  of the plot obtained using g_cluster with –dist option
> -  how is this distribution calculated?
> Thank you in advance,
> All best,
> Michal

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