From: Amir Hajiahmadi Farmahini (
Date: Sat May 22 2010 - 12:15:36 CDT

first thanks for the reply.

Actually, I want to calculate number of specific atoms from surrounding
molecules around a specific pair of atoms in the molecule of interest to
be within a specific distance.
For instance: Suppose in a solution we have carbon dioxide and
MEA(Ethanolamine)dissolved in water.
I want to calculate number of nitrogen atoms from MEA which are within
10 of both oxygens from same CO2 simultaneously. I am going to use RDF
and coordination number analysis tool implemented in VMD. but first I
need to explain for VMD how to consider both oxygen from same molecule
of CO2 as my first selection. Because if I dont confine my selection to
the same CO2 molecule, it will be possible that VMD find some Nitrogens
which are within 10 of two oxygen atoms each from different CO2 molecules.

Best Regards,
Amir Farmahini

Axel Kohlmeyer wrote:
> On Sat, May 22, 2010 at 10:19 AM, Amir Hajiahmadi Farmahini
> <> wrote:
>> Hi,
>> How can I figure out following problem to be able to generate RDF.
>> I need underlying selection as my first selection in VMD to generate RDF:
>> Two or more atoms at them same time have to be selected from "same molecule"
>> in "one selection". To bring a very simple example: both Oxygen atoms from
>> same molecule of carbon dioxide have to be selected as the first selection
>> in RDF to be within a specific distance from Second selection.
>> Second selection can be any atom from another molecules (Not important
>> here).
>> The problem is I was not able to ensure selected atoms are at the same time
>> from same molecule.
> the rdf code knows nothing about molecules. also, your requirements sound
> very odd. can you please elaborate what property you want to calculate?
> even though i am not entirely clear about what you want to do, the
> most promising
> route seems to be that you do a two step procedure. first extract a
> set of "subtrajectories"
> from your original data set that conforms to your first requirement
> and then compute
> the rdfs for each of those and average.
> it may be possible to achieve something similar by setting the user parameter
> for the oxygen atoms in question to specific numbers corresponding to your
> requirements, but that can have unexpected side effects.
> cheers,
> axel.
>> Regards,
>> Amir Farmahini