Hello All
We have been trying to get the charge densities from the trajectory by
using our in-house matlab code, which basically the same as a part of
gmx_potential.c .
z = x0[index[n][i]][axis];
if (z < 0)
z += box[axis][axis];
if (z > box[axis][axis])
z -= box[axis][axis];
/* determine which slice atom is in */
slice = (z / (*slWidth));
(*slCharge)[n][slice] += top->atoms.atom[index[n][i]].q;
However, the charge profiles from the g_potential tool and from our
code show were not the same even for a single structure.
Could you explain how the additional steps might affect?
rm_pbc(&(top->idef),top->atoms.nr,box,x0,x0);
/* calculate position of center of mass based on group 1 */
calc_xcm(x0, gnx[0], index[0], top->atoms.atom, xcm, FALSE);
svmul(-1,xcm,xcm);
Thank you in advance
Sunjoo
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