[gmx-users] RDF calculations for certain atoms in a polymer
mark.j.abraham at gmail.com
Sat Aug 11 12:48:41 CEST 2018
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:
> 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
> Besides there are around 500 of this atom in the system so changing
> something manually is not a good option either.
> Best regards,
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * 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