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

[Dallas Warren]

Make the selection based on the atomtype and resname

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Sat, 11 Aug 2018 at 20:53, 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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