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