Re: Minimization Question

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Mon Nov 12 2018 - 19:50:51 CST

  I removed the restraints on the atoms in the QM region. During the last few steps of minimization, one of the carbon atoms on the benzene ring of my ligand ends up near the center of the ring.

  I moved forward, not worrying to much about the minimization result, and ran the annealing step. I can't get this step to finish. Four hydrogen atoms get stretched quite far, and the job crashes because their velocities are too high. Two of the hydrogens are on a nitrogen on my ligand, the third is on an oxygen on my ligand, and the fourth is on an alpha carbon on one of the valine sidechains. What would cause these hydrogens to move so far during annealing?

Kelly L. McGuire

PhD Scholar

Biophysics

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: Brian Radak <brian.radak_at_gmail.com>
Sent: Monday, November 12, 2018 12:45:43 PM
To: namd-l; McGuire, Kelly
Subject: Re: namd-l: Minimization Question

If this kind of minimization uses the regular NAMD steepest descent/conjugate gradient minimizer (which I think it does) then you almost certainly should use fewer steps. I would rarely recommend more than 200 steps.

Cartesian restraints (ala the horrendously misnamed "constraints" keyword) are very probably recommended, but maybe not on the QM region?

On Sun, Nov 11, 2018 at 8:47 PM McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>> wrote:

  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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