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

[Mahsa]

Hi Mark,

Thank you for your reply!

I tried  gmx make_ndx -f topol.tpr -o index.ndx before and then selected
based on the atom types which worked very well. The only problem is I need
to also compute the RDF for the O of the side chain with the same atom type
as the ester O in the polymer. Then with this approach I get both O types
in a group while I should have them separately. Could you help me with this
problem? I don't know how to specify this one for the RDF calculations.

Best regards,
Mahsa





On Sat, Aug 11, 2018 at 12:22 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

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