Hello PyMOL users, I used gromacs (opls-forcefield) to simulate a peptide, attached here are two energy minimized structures. However, em5 was 40 KJ/mol higher in energy than em4 according to gromacs. When I minimized these two structures using clean function in pymol builder, these structures had exactly the same energy and the structures overlapped. Clearly, there is a change in dihedral angles. Can someone explain what might be going on here?
Many thanks, Neena
em4.gro
Description: Binary data
em5.gro
Description: Binary data
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