[gmx-users] pbc in one direction only for analysis?

[chris.neale at utoronto.ca]

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