Re: Minimization Question

From: Brian Radak (brian.radak_at_gmail.com)
Date: Mon Nov 12 2018 - 20:41:26 CST

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> 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>
> *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> 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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