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: [EMAIL PROTECTED] 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;
}
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];
}
************************************
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