Create atom selection

[Rajorshi Chattopadhyay]

Hello all,

I have a system containing 2 sulphate (SO42-) ions in 100 water molecules. I have .xyz trajectory files containing the atom names and positions.

I want to calculate the survival probability of the water molecules in the first hydration shell of the sulphate ions. For this, I need to create an atom selection containing only the water oxygen atoms in the first hydration shell of the sulphur ion.

I have tried to do this by creating a selection containing only water oxygen atoms. However, I am unable to separate out the water oxygen atoms within the hydration shell from this selection. I see the 'sphzone externalRadius' option, but this selects all atoms within the cutoff radius of the S ion.

Is there a way to create such a selection ?

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With Regards,

Rajorshi Chattopadhyay,

PhD Researcher in Mineralogy/Crystallography,

Institut für Geologie und Mineralogie,

Universität zu Köln, Germany

[Micaela Matta]

Hi Rajorshi,

have you tried creating an atom group with all sulphate atoms, and then using the "around" or "sphlayer" keyword (see geometric selections) to select the water molecules within a certain radius from the sulphate atomgroup? Something like:

water_ag.select_atoms("sphlayer 3.5 global group group_name") 

should select all the water atoms within 3.5 Å of any atom in the group group_name, in your case that would be the sulphate atoms.

Best,

Micaela