From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Mon Nov 12 2018 - 20:52:19 CST
Thanks Brian, I suspected the a bad choice in the quantum region. Not sure how, but my ligand was put into it's one QM region, and I ended up with two QM regions. The sidechains and waters were one QM region, and the ligand was another QM region within the first QM region. So, it looks like two QM calculations were occurring in the same region. I fixed my config file and my qm pdb to place the ligand back with the other QM region, and everything is working great now.
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 7:41:26 PM
To: McGuire, Kelly
Cc: namd-l
Subject: Re: namd-l: Minimization Question
That sounds like a bad starting structure or otherwise bad choices in the quantum model and/or quantum region. If minimization is causing your system to distort, you probably have to look somewhere besides your equilibration protocol.
On Mon, Nov 12, 2018 at 8:50 PM McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>> wrote:
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<mailto: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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