[gmx-users] Alpha-Helix Dipole

[gtroiano at if.usp.br]

 Just one more thing, David. I read the manual, but I couldn't realize: is the
average dipole, (at the top of the g_dipoles output) the overall dipole of the
system? (also in the adip.xvg, plotted against time). Because all I want to
know is whether the system has a low dipole moment (which in the case of
polyala+h2o, the average is 2.3 D)

 Gustavo


> gtroiano at if.usp.br wrote:
> >  Hi David
> >
> >  Thank you very much for the reply! So, which group, in the end, shall I
> select
> > in g_dipoles to see the dipole? And how to use trjconv after editconf the
> way
> > you told me? (the input/output of editconf is a .gro file and of trjconv is
> > .trr/.xtc files) And whose group shall I select in the least squares/output
> > prompts in trjconv -fit trans+rot?
> >
> >  Thank you very much,
> >  Gustavo
> >
> >
> I would do both the helix backbone, and the entire helix, so that you
> can test whether the sidechains compensate for the net dipole or the
> other way around. You could also look at the net dipole of the water
> with resect to the helix.
>
> As for trjconv, please read the manual about aligning structures
> (trjconv -h)
>
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>
> --
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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