[gmx-users] Protein Dipole moment

[Qiao Baofu]

no. the com is not used in the g_dipoles.

The simplest way to use com is to replace the content of the { void
mol_dip() } with the following code.

************************************
  int  k,kk,l;
  real q,m,m_sum,q_sum;

  q_sum = 0;
  m_sum = 0;
  for(k=k0; (k<k1); k++) {
    kk = ma[k];
    q_sum += atom[kk].q;
    m_sum += atom[kk].m;
  }

  clear_rvec(mu);
  for(k=k0; (k<k1); k++) {
      kk = ma[k];
      m = atom[kk].m;
      q = atom[kk].q;
      q = e2d(q-m*q_sum/m_sum);
      for(l=0; l<DIM; l++)
          mu[l] += q*x[kk][l];
  }
************************************



2007/3/5, Georgios Patargias <G.N.Patargias at leeds.ac.uk>:
>
> Hello
>
> Does g_dipole take the center of mass of a molecule as the origin when
> calculates its dipole moment?
> If yes, is it the com at t=0 that is used or is it re-calculated for every
> frame?
>
> I had look at the source code but it wasn't very clear to me.
>
> Thank you very much in advance.
>
> Best wishes
> George
>
> Dr. George Patargias
> Polymer IRC Group
> University of Leeds
> Leeds, LS2 9JT, UK
>
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-- 
Sincerely yours,
**********************************************
Baofu Qiao, PhD
Frankfurt Institute for Advanced Studies
Max-von-Laue-Str. 1
60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529
**********************************************
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