[gmx-users] emtol criterion

[Kevin Boyd]

> For GROMACS, I think the emtol
> value should be reported, but this varies by personal preference in most
> papers, unfortunately.

I had thought that emtol had no particular significance for minimizations
used to set up typical MD simulations, as long as the system was
sufficiently minimized as to not explode. Is there any evidence that stable
simulated systems behave differently based on the minimum energy they
achieved during minimization?

On Wed, Nov 27, 2019 at 4:05 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/27/19 12:39 PM, Christos Deligkaris wrote:
> > dear all,
> >
> > I am trying to decide on a reasonable cutoff for emtol.
> >
> > The Gromacs manual (section 3.10 on energy minimization) states that a
> > reasonable criterion for emtol can be found from the rms force a harmonic
> > oscillator would exhibit at room temperature (Equation 3.125). For a weak
> > oscillator (100 cm^-1) a force of 7.7 kJ/mol/nm is obtained. This number
> is
> > consistent with the default criterion of 10.0 kJ/nm/mol. It is not clear
> to
> > me how the value of 100cm^-1 was chosen in this example though.
>
> I can't comment directly on this aspect, but a value of 100 cm^-1 is
> about 10x lower than most bond vibrations in biological systems, so this
> would correspond to some slower, low-amplitude motion in, e.g. a
> protein. So in essence, the back-of-the-envelope math suggests forces
> converging below this value would put you at an energy minimum with only
> very low-frequency modes. In practice, this is a very strict criterion
> and often difficult to achieve in mixed precision (and sometimes even in
> double).
>
> > Using a frequency of 1900cm^-1 and 7 amu reduced mass for CO stretching I
> > got 122 kJ/mol/nm which appears to be more consistent with the criterion
> of
> > 1000 kJ/nm/mol used in the lysozyme tutorial:
> > http://www.mdtutorials.com/gmx/lysozyme/05_EM.html
> >
> > In the literature I see the number of minimization steps (nsteps)
> reported
> > but not a specific criterion.
>
> In my experience, this generally varies by either (1) software or (2)
> the precision with which the authors report their settings. You can say
> that there were "5000 steps of steepest descent minimization" in
> GROMACS, but more often than not, that's what is set as nsteps but not
> actually used. Other software (CHARMM, AMBER, etc) will gladly perform
> exactly as many steps of SD as you tell it to rather than bailing out
> after a convergence criterion is reached. For GROMACS, I think the emtol
> value should be reported, but this varies by personal preference in most
> papers, unfortunately.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
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>
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>
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