I'm performing a QM/MM energy minimization with ABNR in c38b2 with the CHARMM/Turbomole interface.
The system is a solvated protein/NA complex where I have fixed everything except a sphere within 15A of an active site residue.
I'm using the CHARMM36 parameters.
The calculation is with:
ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch
BYGRoup NOEXtnd NOEWald
CUTNB =160.000 CTEXNB =999.000 CTONNB =100.000 CTOFNB =120.000
CGONNB = 0.000 CGOFNB = 10.000
WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000
NBXMOD = 5
If I do the energy minimization I observe, that there are certain upticks in the energy(see image, plotted are the value directly behind the "MINI>"). The total trend however is to a lower energy. What could be the reason for these upticks?