Hi,
Checked and looks reasonable now. Thanks again.
El lun., 28 ene. 2019 a las 21:00, Daniel Roe (<daniel.r.roe.gmail.com>)
escribió:
> Hi,
>
> I've addressed this issue in the GitHub version of cpptraj (see
> https://github.com/Amber-MD/cpptraj/pull/660). If you get a chance,
> please try the GitHub version and see if your results make more sense
> now.
>
> -Dan
>
> PS - I've added an issue to GitHub to remind me about the "perhead" stuff.
>
> On Mon, Jan 28, 2019 at 12:27 PM Stephan Schott <schottve.hhu.de> wrote:
> >
> > Thanks for the heads up.
> >
> > The first is that 'lipidorder' cannot distinguish between the two OL
> tails
> > > of each
> > > lipid, so the results are for all OL residues, whereas 'lipidscd' does
> > > results for each separate tail.
> >
> >
> > I was aware of the calculation difference, but if that would have been
> the
> > relevant difference, the error in lipidorder should have been higher, as
> > the average goes over sn1 and sn2 tails, and not the other way around.
> >
> > In your system there are also
> > > different linkers for some lipids - I may need to update 'lipidscd' to
> > > distinguish based on this as well.
> > >
> >
> > A "perhead" flag would be cool :O
> >
> >
> > >
> > > The second difference is in how the standard deviations are
> > > calculated. In 'lipidorder', the standard devation is for the averaged
> > > SCD values, whereas for 'lipidscd' the standard devation is for all
> > > individual SCD values. The averages work out to be the same, but this
> > > is why the magnitude of the current 'lipidscd' s.d. values are much
> > > larger than for 'lipidorder'. I'm pretty sure that what people want
> > > typically is what 'lipidorder' reports (i.e. for a single frame the
> > > s.d. for each position should be zero.). This also explains the
> > > unexpected behavior of 'lipidscd' s.d. values that was reported
> > > eariler.
> > >
> >
> > Thanks for looking into it!
> >
> > Cheers,
> >
> >
> > --
> > Stephan Schott Verdugo
> > Biochemist
> >
> > Heinrich-Heine-Universitaet Duesseldorf
> > Institut fuer Pharm. und Med. Chemie
> > Universitaetsstr. 1
> > 40225 Duesseldorf
> > Germany
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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>
--
Stephan Schott Verdugo
Biochemist
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf
Germany
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Received on Tue Jan 29 2019 - 08:30:03 PST
