[gmx-users] Alpha-Helix Dipole

[gtroiano at if.usp.br]

 Hi David,

 I tried to use the option -mutot in g_energy, but all I get is the component
dipoles. They match what I've got in the file Mtot.xvg from g_dipoles, which is
really high (for all the system: water+ polyala helix, fluctuates between 100
and 300 D), but in adip.xvg (the average) the value in each time is very low
(around 2.3 D). The index file contains only the standard options (protein,
SOL, backbone, etc..) and when I try to select backbone (e.g. in g_dipoles) it
gives the fatal error: "The index group is not a set of whole molecules". Why
is the Mtot like this and what exactly does the average mean?
 Anyway, thanks for all the guidance, it helped a lot! I tried to make it
objective now and this is the last question I send you, for not wasting your
time! If I can't conclude anything, can you send me any reference, or some
exercises which I could compare some results and see if what I'm doing is right
or what to expect from the dipole calculation?  (I think that the structures are
ok for the QM, but just I wanted to confirm if that situation is the closest
that we have for the helix in water)

 Thank you very much (sorry if any of the questions seemed stupid!)
 Gustavo



> gtroiano at if.usp.br wrote:
> >  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)
> >
>
> depends on your index file. the total dipole is also stored in the
> energy file, so you can run g_energy to get it out, or g_dipoles -enx to
> compute dielectric constants etc.
>
> >  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)
> >>
> >>   Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >>
> >>
> >> --
> >> 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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> >
> >
> >
> >
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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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