[gmx-users] Protein Dipole moment

Georgios Patargias G.N.Patargias at leeds.ac.uk
Tue Mar 6 17:22:13 CET 2007

Thanks for your reply Qiao! I was wondering what is the origin 
that the g_dipoles uses if not the com? 

Would it make any sense to generate a trajectory with the protein 
fitted to the Calphas before we calculate the dipole moment? 
Dr. George Patargias
Polymer IRC Group
University of Leeds
Leeds, LS2 9JT, UK

-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of Qiao Baofu
Sent: Tue 3/6/2007 8:08 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Protein Dipole moment
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;

  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];

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