GROMACS version:2019
GROMACS modification: No
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Recently, I use gmx rdf command to calculate the RDFs. However, I am confused by
" -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
"
what the different res_com, mol_com, part_res_com, mol_cog, and so on? Where could I find some material about their difference?
When you calculate RDF, you need to calculate the distance between the two groups. Then, RDF is calculated by histogramming the calculated distances. A group can consist of single atom, molecule, residue, etc. If a group has more than one atom, then the center of mass (com) or the center of geometry(cog, mass unweighted com) is considered. Out of two groups, the first one is a reference group and second one is the output group.
When you calculate COM/COG of a group of atoms, they need to be unwrapped (whole). If your trajectory has already been unwrapped (e.g. using trjconv -pbc whole), you would use res_com/mol_com (per se), otherwise, you need to ask gromacs explicitly by whole_res_com/whole_mol_com.
Thanks for your kind reply. I got some information from gmx selections command
For Whole, it said " [TT]whole_[tt] calculates the centers for the whole residue/molecule,",
" even if only part of it is selected."
it seems that the whole is not used to eliminate the PBC effect. If I do not misunderstand, it is used to calculate the center of mass of whole residue/molecule, even if one only chooses an atom of one residue/molecule.
For the gmx rdf command, the item “-[no]rmpbc (yes)” was used to make molecules whole for each frame.
So, does it means that I could use -rmpbc yes to instead the trjconv -pbc whole?
I am confused by your explanation and help information.