GROMACS

static void center_x_com(int ecenter,rvec x[],matrix box,int n,int nc,atom_id ci[],t_atom atom[])

{

    int i,m,ai;

    rvec com,box_center,dx;

    real mtot;

    mtot=0.0;

    com[0]=com[1]=com[2]=0.0;

    if (nc > 0) {

        for(i=0; i<nc; i++) {

            ai=ci[i];

            for(m=0; m<DIM; m++) {

                com[m]+=atom[ai].m*x[ai][m];

            }

            mtot+=atom[ai].m;

        }

        calc_box_center(ecenter,box,box_center);

        for(m=0; m<DIM; m++)

            dx[m] = box_center[m]-com[m]/mtot;

        for(i=0; i<n; i++)

            rvec_inc(x[i],dx);

//fprintf(stderr,"want %f %f %f but have %f %f %f\n",box_center[0],box_center[1],box_center[2],

    }

}

                            if (bCenter){

                                //center_x(ecenter,fr.x,fr.box,natoms,ncent,cindex);

                                center_x_com(ecenter,fr.x,fr.box,natoms,ncent,cindex,atoms->atom);

                            }