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

[Mahsa]

Thank you for your reply!

Best regards,
Mahsa

On Mon, Aug 13, 2018 at 2:47 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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