Gmx rdf options and usage

User discussions
1

GROMACS version:2020
GROMACS modification: No
I have done MD simulation for a DNA_DNA double helix molecule and would like to study the the rdf for the helix. since I am following a paper, in which they report the rdf, I am trying to confirm the results and then make amendments wıth my own molecules.

I came across several posts but I would like to clarify about the options.

For example I want to find the distance between C5 of two adjacent T and T bases. I know their atom numbers and have created an index file that contains all the atoms of the Ts.

How do I add the specific base İDs to specify the specıfic pairs

the command line I have is

gmx rdf -f name.xtc -s topol.tpr -ref 12DT -selrpos C5 -sel 13DT -seltype C5 -n name.ndx -o T12-13.xvg

İ know it is incorrect but how do I add the proper options?

Kindly help.

Thank you

Ayesha

2

Hello again,
I managed to get the rdf function working by creating the index file of the atoma I wanted to use as teh groups and got my output file.

Now the problem I am facing is the y-axis that has values of more that 1000.

based on the tutorials and examples available online I shoudl be getting the probability values 0-1. Now I am confused as to what does the y-axis signify.

I would appreciate some insight into the matter.

Thank you
Ayesha