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

[Mark Abraham]

Hi,

You need a composite selection, eg of an atomtype and residue type or
molecule type. Make a selection of the atomtype and another of whatever
seems suitable, and combine them.

Mark

On Sat, Aug 11, 2018, 13:53 Mahsa <ebadi.mahsa at gmail.com> wrote:

> 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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