Gmx rdf selection options

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1

GROMACS version:2018

Hi All, I have performed a simulation of 23 fullerene molecules in water. I would like to calculate the radial distribution function or g(r) between center of mass of a fullerene and Ow-atom of water molecules and also the rdf or g(r) between the fullerene-fullerene centers of mass. I have an index group containing all the fullerene atoms in one group. If I know correctly, by default gmx rdf calculates rdf from a reference group and a selection group taking all atoms into consideration. I am interested in calculating rdf using center of mass between fullerene-fullerene and fullerene-water. I have seen that gromacs has multiple ways to provide which atoms are to be taken into consideration:

-selrpos (atom)
Selection reference positions: atom, res_com, res_cog, mol_com,
mol_cog, whole_res_com, whole_res_cog, whole_mol_com,
whole_mol_cog, part_res_com, part_res_cog, part_mol_com,
part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
-seltype (atom)
Default selection output positions: atom, res_com, res_cog,
mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com,
whole_mol_cog, part_res_com, part_res_cog, part_mol_com,
part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog

However, I am a bit confused with which one of this options to use and also can anyone please explain the meaning of the above mentioned keywords: selrpos and seltype. Any help is much appreciated, thank you

2

Hi,
gmx rdf calculates radial distribution functions from one reference set of position (set with -ref ) to one or more sets of positions (set with -sel ).
-selrpos is used to define the type of position for the reference group
-seltype is used to define the type of position for the selection

In your case given an index file with a group for Ow atoms [ Ow ] and one with the fullerene molecules [ FUL ]
To generate the rdf between the fullerene-fullerene com you can use the following command
gmx rdf -f name.xtc -s topol.tpr -ref FUL -selrpos mol_com -sel FUL -seltype mol_com -n name.ndx -o rdf_FUL-FUL.xvg
To generate the rdf between the fullerence (COM) and the Ow atoms:
gmx rdf -f name.xtc -s topol.tpr -ref FUL -selrpos mol_com -sel Ow -seltype atom -n name.ndx -o rdf_FUL-Ow.xvg
Does this answer your question?
\Alessandra

1 Like
3

Yes this answes my qustion and thank you for your suggestions.