Hello all
This is regarding the gmx rdf and excl flag.
When the flag is included, the exclusions are read from the topology. This means that for nrexcl=3, atoms three bonds away are excluded in the rdf. Supposing if the atoms in the molecule are bonded, as in the case of carbons atoms in the back bone of long polymer chain and I wish to calculate the inter-rdf of the carbon atoms (system has many chains) how would one go about doing it ?
A way would be to generate a new tpr file with the exclusions I want and use gmx rdf.
Is this the right approach ? or are there any other ways.
Suggestions are greatly appreciated
Thanks
Arun