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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
