From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Sun Nov 11 2018 - 19:46:19 CST
Usually, during a normal MM simulation, I run the minimization for 1,000 to 2,000 steps. Now, with a QM/MM simulation, using PM7, MOPAC, and GPUs, I can minimize for 1,000 steps in 25 minutes. However, looking at the minimization trajectory, in the QM region some of the sidechain atoms move drastically, causing their bond to stretch really far. I tried restraining the whole sidechain, but the it still happens.
1) Should I not use restraints on the atoms in the QM region?
2) Should I use fewer steps during minimization?
3) Could it be PM7, maybe use a non-semi-empirical theory for minimization?
Same questions for the annealing and equilibration steps...
Kelly L. McGuire
Department of Physiology and Developmental Biology
Brigham Young University
Provo, UT 84602
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