Re: [AMBER] lipidscd S.D.

From: Daniel Roe <>
Date: Mon, 28 Jan 2019 11:53:42 -0500

OK, I think I have a handle on what's going on here. There are two
main differences between 'lipidorder' and 'lipidscd'. 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. In your system there are also
different linkers for some lipids - I may need to update 'lipidscd' to
distinguish based on this as well.

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

I'm working on a correction now. Thanks for the report.


On Tue, Jan 22, 2019 at 7:19 PM Daniel Roe <> wrote:
> Hi,
> This seems strange, and is something that has been reported at least
> once before, but I've never been able to reproduce it. Could you
> possibly send me off-list files I can use to reproduce the behavior in
> cpptraj (topology, trajectory, input)? Thanks
> -Dan
> On Tue, Jan 22, 2019 at 9:44 AM Stephan Schott <> wrote:
> >
> > Hi everyone,
> > I had some order parameter calculations with lipidorder, but I wanted to have the per-tail component without the hassle of defining the residue ids. I tried lipidscd, and the values seem to be right, but the SD is in the same order of magnitude as the order parameter itself. The SD of lipidorder was quite small, on the other hand. Anything particularly different going on under the hood, or something I'm missing?
> > Cheers,
> > --
> > Stephan Schott Verdugo
> > Biochemist
> >
> > Heinrich-Heine-Universitaet Duesseldorf
> > Institut fuer Pharm. und Med. Chemie
> > Universitaetsstr. 1
> > 40225 Duesseldorf
> > Germany

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