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

Mark Abraham mark.j.abraham at gmail.com
Sat Aug 11 12:48:41 CEST 2018


Making a selection with a tool like gmx select or gmx make_ndx is a good
way to select e.g. by atomtype.


On Sat, Aug 11, 2018, 12:58 Mahsa <ebadi.mahsa at gmail.com> wrote:

> Hello,
> 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
> atoms?
> Besides there are around 500 of this atom in the system so changing
> something manually is not a good option either.
> Best regards,
> Mahsa
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