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

Jennifer Williams Jennifer.Williams at ed.ac.uk
Tue Aug 31 14:37:17 CEST 2010

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


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