[gmx-users] Average RDF

[Bratin Kumar Das]

You need to create the .ndx file of all oxygen you need and calculate the
rdf ..Providing the .ndx file by -n flag

On Wed 28 Aug, 2019, 10:40 PM Maryam Sadeghi, <maryam.sadeghi.90 at gmail.com>
wrote:

> Hi All,
>
> I am simulating a single chain of Polyethylene Glycol (PEG9 terminating
> with -OH groups) in water, and I need to calculate the RDF for the terminal
> Oxygens & O-water (Ot-Ow) as well as the ether Oxygens within the chain (in
> my case 9 Oxygens) and O-water (Oe-Ow).
> I have calculated the Oe-Ow RDF for each single O within the chain, but I
> am actually looking for the average RDF of all ether Oxygens. Could anyone
> tell me how I can compute an average RDF in GROMACS for all the ether
> Oxygens within the chain?
>
> Thank you
> Maryam
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