[gmx-users] RDF calculations for certain atoms in a polymer

Mahsa ebadi.mahsa at gmail.com
Sat Aug 11 11:57:28 CEST 2018


I would like to calculate the RDF between some ions and oxygen atoms of a
polymer. The polymer has ester functional group with two different atom
types O and OS according to GAFF. It has also a side chain with ethereal
oxygen which has the same atom type as the ester part. How can I specify
the O of the side chain in the index file to tell it apart from the other O
Besides there are around 500 of this atom in the system so changing
something manually is not a good option either.

Best regards,

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