Hi there I'm working with gromacs for ligand-protein interaction simulation. I have run MD for docked complex and now there is a problem with trajectory visualization by VMD. The ligand has left binding site circulating around the protein. I tried to fix the problem by making index and extract the first frame from the trajectory to use as reference and also running "-center", "no jump", "no pbc", "-fit rot" but the problem still exists. I'm quite confused. Should I execute fixing command in the special order? Which group is more preferred to be located at the center,Protein or system(non-solvent)? I would be grateful if you could help me in this matter. -- Homa Ahmadi Shahed University Faculty of Basic Sciences Alternative email> h.ahm...@shahed.ac.ir <h.ahm...@ast.ui.ac.ir> -- Gromacs Users mailing list
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