Re: Minimization Question

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Mon Nov 12 2018 - 15:35:57 CST

   Hey Gerard, sorry I should have clarified. In this case, the QM/MM simulation has a ligand without copper. The only atom types in this ligand are C, O, N, and H. Part of the ligand, however, is a benzene ring, so it has double bonds. So, it's really the hydrogens on the valine sidechains in the protein that is exhibiting this phenomenon after minimization. I did just equilibrate my system for 5 nanoseconds with regular MM, and then used the last frame of that equilibration as my starting point for this QM/MM. I ran 100 steps of minimization and the valines appear fine now. But, the one of the carbons in the benzene ring moves inward toward the center of the ring, thus distorting the ring quite a bit.

Kelly L. McGuire

PhD Scholar

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: Gerard Rowe <GerardR_at_usca.edu>
Sent: Monday, November 12, 2018 12:08:00 PM
To: namd-l_at_ks.uiuc.edu; McGuire, Kelly
Subject: Re: Minimization Question

I had similar issues with PM7 QM/MM calculations with my model system. I don't know that it's particularly robust when dealing with open shell systems with unusual metal geometries. I frequently had SCF failures with a high-spin sextet system, and things weren't much better when I simplified to a low-spin doublet. As far as restraints go, you might want to inspect the force constants produced by the PM7 calculation. If they are unreasonably high, they can overcome the restraint placed on the atoms unless your restraint barrier multiplier is also unreasonably high.

Unfortunately, my only recourse was to fall back to DFT. Is it possible to substitute your copper with zinc in the semiempirical calculations? They're similar as long as you don't need to monitor redox behavior.

________________________________
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of McGuire, Kelly <mcg05004_at_byui.edu>
Sent: Sunday, November 11, 2018 8:46:19 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: Minimization Question

  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

PhD Scholar

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

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