[gmx-users] traj comparison

[giacomo de mori]

Dear Gromacs users,
we would like to compare two trajectories of two peptides with the same
sequence, one containing an SS bond and the other without it (different
topology files). We would like to compare them to a common backbone
structure and obtain matrix in .xpm format of comparison values of each
structure in the 1st trajectory with respect tothe other (like -f2
option in g_rms). Is there an easy way to overcome the different
topology problem?
Thanks in advance
Giacomo