RDF calculations

User discussions
1

GROMACS version: 2020.6
GROMACS modification: Yes/No

Deal All,

I want to calculate RDF, i have one component membrane contain single lipids, water, and ions. Firstly, Need just clarification about, during indexed preparations, should i chose all the lipid molecules of the system as single index group or any single molecule selections will work as -ref options and for water molecule is it correct to chose O* for -sel options. Secondly, which selections options suitable for me to calculate RDF:

-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

Thank you in advance

2

Depends on what type of RDF you want. Maybe make a system with 2 lipids and compute the RDF on a single frame and then compare your values from the gromacs tool to distance evaluations out of VMD or simple math on the input structure? Then try a system with 3 lipids in a similar test.