[gmx-users] g_density

[chris.neale at utoronto.ca]

Dear Matthias:

Did you run trjconv -center -pbc mol at some point before running  
g_density? With pbc, there are multiple ways to put the center of a  
system at the center of the box. This can lead to having the water  
slab in the center of the unit cell and the bilayer on the top and  
bottom z.

Without seeing the commands and the output, it is hard to say any more.

Chris.

-- original message --

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