spoel at xray.bmc.uu.se
Thu Jun 12 19:25:01 CEST 2003
On Thu, 2003-06-12 at 18:40, Carmen Domene wrote:
> > Dipole moment (Debye)
> > ---------------------
> > Average = 1101.3528 Std. Dev. = 151.9949 Error = 75.9975
> > The following averages for the complete trajectory have been calculated:
> > Total < M_x > = 2758.17 Debye
> > Total < M_y > = 2620.62 Debye
> > Total < M_z > = 2073.38 Debye
> > This is what you want to look at: 1 Debye is roughly 48 e nm, so what
> > you have here (M_x) is roughly 56 e nm, or, if your protein is 2 nm,
> > this would correspond to +14 on one side and -14 on the other side. Is
> > it that much charged?
> Sorry, but could you tell me the meaning of the Average value that comes
actually I don't know, check the source it's quite easy.
> from g_dipole and also how you calculate the dipole of a charged system
> with g_dipole? Do you calculate the dipole wrt the center of mass of the
> system, a geometrical center or maybe something else?
We don't take a total charge into account, you just get sum q r, if you
want to know with respect to the center of mass, use editconf to center
your molecule at the origin. Of course as long as you have a charge it
is still arbitrary. You could try to center the protein at the center of
charge, i.e. take the dipole above, divide by twelve* 48 and move the
molecule along that vector in the opposite direction..
> My protein has a total charge of +12.
> Thanks, Carmen
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
Dr. David van der Spoel, Dept. of Cell and Molecular Biology
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
More information about the gromacs.org_gmx-users