Trjconv - dimer protein-ligand
I'm new in GROMACS. I have ran a MD simulation of a dimer protein where each monomer is bound with a ligand.
However, the protein interacts with its image for the presence of PBC. Thus, the protein seems to have long bonds and ligands were not in the binding site. I have tried the trjconv command with different combinations, but this does not solve the problem. In fact, I was able to recenter e wrap the protein and ligands, but in the last frame, ligands are put far away the binding pocket. How could I solve this issue? Moreover, could the trjconv influence the following analyses (For example the calculation of RMSD, RMSF, hydrogen bond, ...)?
Thank you in advance.