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

[Mahsa]

Dear Mark,

Could you please comment on my previous question? I would really appreciate
it.

Best regards,
Mahsa

On Sat, Aug 11, 2018 at 12:52 PM, 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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