[gmx-users] Alpha-Helix Dipole

[gtroiano at if.usp.br]

 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!

 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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