[gmx-users] acceptable errors in density and melting point

[Victor Rosas Garcia]

That's a good point Vitaly.  Different properties need different tolerances.

2015-10-15 20:50 GMT-05:00 Vitaly V. Chaban <vvchaban at gmail.com>:

> Density discrepancy of 12% is unacceptable for any substance.
>
> Melting point is better, if T is in K.
>
> Different properties assume different healthy discrepancy thresholds.
>
>
>
>
>
> On Thu, Oct 15, 2015 at 6:02 PM, Victor Rosas Garcia <
> rosas.victor at gmail.com
> > wrote:
>
> > Thanks Justin.  That's what I needed to know.
> >
> > Victor
> >
> > 2015-10-15 15:58 GMT-05:00 Justin Lemkul <jalemkul at vt.edu>:
> >
> > >
> > >
> > > On 10/15/15 4:51 PM, Victor Rosas Garcia wrote:
> > >
> > >> hello everybody,
> > >>
> > >> Let us say that I have a topology for a small organic molecule. When
> > >> running NPT equilibration to determine the density of the solid, I
> get a
> > >> 12% error vs experiment. When determining the melting point using
> > >> simulated
> > >> heating, my error is about 15% vs experiment.  Are these errors too
> > high?
> > >> good enough? I have been searching for papers that discuss acceptable
> > >> errors for molecular dynamics parametrizations but so far have not
> found
> > >> much. Any pointers?
> > >>
> > >>
> > > Acceptable thresholds vary.  We aim for an error of 2% of less.  I
> would
> > > say your errors are too high.
> > >
> > > -Justin
> > >
> > > --
> > > ==================================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 629
> > > University of Maryland, Baltimore
> > > 20 Penn St.
> > > Baltimore, MD 21201
> > >
> > > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > > http://mackerell.umaryland.edu/~jalemkul
> > >
> > > ==================================================
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