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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
