[gmx-users] gmx rdf with surf option

[zeineb SI CHAIB]

Dear GMX users,

I have a question regarding GMX RDF and I apologize if my question is too basic.

My trajectory consists of a dimer inserted in a membrane with an explicit water/ion environment. I would like to compute the distribution of the center of mass of lipid molecules to the surface of the receptor.

My first test consisted of the following command:

1) gmx rdf -f traj.xtc -s md.tpr -n index.ndx -o rdf_T1.xvg -surf  mol -seltype whole_res_com


I got the following error:

Inconsistency in user input: -surf only works with -ref that consists of atoms
When I run again the same command line but with -selrpos, it works "fine"
2) gmx rdf -f traj.xtc -s md.tpr -n index.ndx -o rdf_T1.xvg -surf mol -selrpos whole_res_com
I know that COMs are not supported with -surf. But -seltype is supposed to be related to "the type of selection for the atom or group, residue, etc, we want to calculate the rdf for" no?. I can't understand why I got this error when using -seltype with -surf option. Any comment on this?
In another test I tried this:
3) gmx rdf -f traj.xtc -s md.tpr -n index.ndx  -o rdf_g15.xvg -surf mol -ref 'protein' -sel ''whole_res_com of group 15''
this one works fine but the output is different from the previous command (2). Although for me I was expecting the same results?!
If none of these commands is correct, can you please tell me which option I can use in order to compute the RDF as the distribution of COM of lipid molecules to the surface of the protein, please?
Thanks a lot.