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
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Received on Mon Jan 28 2019 - 12:00:03 PST
