[gmx-users] Alpha-Helix Dipole

[gtroiano at if.usp.br]

 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

> gtroiano at if.usp.br wrote:
> >  Hello
> >
> >  I'm a beginner user of GROMACS, and I'm currently trying to simulate some
> alpha
> > helices in an explicit water box to extract some initial structures for
> > subsequent quantum mechanical calculations (which uses pbc as well).  I'd
> like
> > to know if there's a way to check if the dipole moment of the protein
> backbone
> > is screened by the water, the way it should be, because if not, the results
> > from QM will be incorrect for what I want to observe. I checked the results
> > with g_dipoles_d and below is what I got, for 500ps 300K NVT MD of a 20
> residue
> > polyalanine in a box of  1813 water molecules (total of 5651 atoms, 1nm
> from the
> > edges of the helix), but I'm not certain where to look to decide if it's
> correct
> > (of course, a frame won't necessarily have a zero dipole moment, but maybe
> it
> > seems too high? If you look at the Mtot.xvg, the total dipole is between
> 240
> > and 60 Debye). Any help would be appreciated!
> >
> did you select just the helix backbone for this calculation? probably
> not, and then you are looking at the water. in addition you probably
> want to align the helix to the box otherwise you are looking at the
> average of a moving helix. editconf -princ and then use trjconv -fit
> rot+trans to fit the trajectory on the first structure.
>
> >  Thanks in advance,
> >  Gustavo
> >
> >
> > Dipole moment (Debye)
> > ---------------------
> > Average  =   2.3041  Std. Dev. =   1.2691  Error =   0.0042
> >
> > The following averages for the complete trajectory have been calculated:
> >
> >  Total < M_x > = 39.2483 Debye
> >  Total < M_y > = -54.7993 Debye
> >  Total < M_z > = 59.1645 Debye
> >
> >  Total < M_x^2 > = 9509.68 Debye^2
> >  Total < M_y^2 > = 14277.5 Debye^2
> >  Total < M_z^2 > = 17721.9 Debye^2
> >
> >  Total < |M|^2 > = 41509.1 Debye^2
> >  Total < |M| >^2 = 8043.83 Debye^2
> >
> >  < |M|^2 > - < |M| >^2 = 33465.3 Debye^2
> >
> >
> >
> > ----------------------------------------------------------------
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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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