Dear Gromacs users: I recently tried some MM/PBSA stuff using the rerun function of mdrun and GBSA model. All water molecules are stripped off the trajectory file.
However, when I examine the different energy term, it is disturbing that short range vdw energy of some snapshot are very high (> 1000 kj/mol) while others snapshots typically have a value around -2000 kj/mol. It is more disturbing that if I do a fitting or pbc nojump on the trajectory first, I will get very different short range vdw for some of the snapshots. All other energy terms are un-affected. I believe fitting or no-jump processing shall not change the energy at all. Any one has idea about this?
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