[gmx-users] g_density

[Matthias Schmidt]

Hi,

I have aligned a trajectory to a reference structure and have now run
g_density on both the original and the aligned trajectory in order to
find the bilayer headgroup position and the bilayer thickness.

g_density works fine with the original trajectory but there seems to
be a bug when running it to the aligned structure (Alignment done
using trjconv -fit progressive).

The density is calculated along the z direction (-d Z). The density
for positive z is calculated correctly, but the density for negative z
is shifted about 15nm to to the top end of the box size, as if the
density distribution along the z-axis were discontinuous.

Other then stitching the data together by hands, are there any obvious
better solutions?

Thanks,

Matthias