Computing Binding Free Energy Approach #482
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josephDeluna
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I've done multiple dynamics simulation of different ligands with the same protein, use "gmx trjconv -center" and computed their respective binding free energies. However as I visualize those protein-ligand complexes, I've noticed that some of them split the protein in two and jumps outside of the box. So I use "gmx trjconv -nojump" to fix those complexes.
My questions are:
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