[PyMOL] Energy minimization in Pymol

[Neena S. E. <nee...@gm...>]

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