[gmx-users] trjconv reference structure (bug?)

[Mikko Huhtala]

Thanks for the replies. Using a tpr for the same system as reference
surely is convenient, but my problem was that I had never run
simulations for the reference system at all. I realized I did have a
different number of hydrogen atoms for the reference and trajectory
protein structures, which is why I got very strange fitted
trajectories. But even when I fix this so that the numbers of protein
atoms match exactly, trjconv still never finishes the fitting unless
solvent etc. are also in the ref gro. I haven't looked at the source
of trjconv. Nguyen Hoang Phuong's description of what is going on
seems correct to me.

Mikko