Re: Minimization Question

From: Brian Radak (brian.radak_at_gmail.com)
Date: Mon Nov 12 2018 - 13:45:43 CST

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*
>
>
>

This archive was generated by hypermail 2.1.6 : Wed Dec 04 2019 - 23:20:21 CST