[gmx-users] Alpha-Helix Dipole
David van der Spoel
spoel at xray.bmc.uu.se
Tue Aug 28 22:50:18 CEST 2007
gtroiano at if.usp.br wrote:
> 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,
> 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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