[gmx-users] RDF calculations for certain atoms in a polymer
ebadi.mahsa at gmail.com
Sat Aug 11 12:53:12 CEST 2018
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.
On Sat, Aug 11, 2018 at 12:22 PM, Mark Abraham <mark.j.abraham at gmail.com>
> 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
> > --
> > Gromacs Users mailing list
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users