It's a messy solution, but you could 1. run trjconv so that your cylinder is in the unit cell 2. convert your trajectory to .gro files 3. massively expand the x and y dimensions of each .gro 4. join the .gros to a .xtc 5. g_rdf
You could also use template.c to write a program that does this directly to a .xtc file.
Chris. -- original message -- Dear gromacs users I have surface groups anchored on a cylindrical pore wall (similar to a carbon nanotube). The pore runs along the z direction. I am trying to determine to what extent my surface groups are clustered together and was thinking of using g_mindist and/or g_rdf for this analysis. I usually work with periodic boundary conditions in all 3 directions for MD runs. The problem I have is that I want to use periodic boundaries only in the z direction and not the x and y for the anaysis. I.e I dont want the surface groups in my pore to see other surface groups in neighbouring cells in the x or y direction. From what I can see, the options with g_rdf is either to have pbc in all 3 directions or not at all. Does anyone know a way around this? I am analyzing one pdb file and not a trajectory. I am using gromacs 4.0.7 Thanks -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
