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fix: use correct ref coords for RMSD Jacobian #884

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fix: use correct ref coords for RMSD Jacobian #884

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8 changes: 5 additions & 3 deletions src/colvarcomp_distances.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1006,11 +1006,11 @@ void colvar::rmsd::calc_gradients()
0.0;

// Use the appropriate symmetry permutation of reference positions to calculate gradients
size_t const start = atoms->size() * best_perm_index;
size_t const best_perm_start = atoms->size() * best_perm_index;
for (size_t ia = 0; ia < atoms->size(); ia++) {
const cvm::atom_pos pos_ia(
atoms->pos_x(ia), atoms->pos_y(ia), atoms->pos_z(ia));
const cvm::rvector grad = (drmsddx2 * 2.0 * (pos_ia - ref_pos[start + ia]));
const cvm::rvector grad = (drmsddx2 * 2.0 * (pos_ia - ref_pos[best_perm_start + ia]));
atoms->grad_x(ia) = grad.x;
atoms->grad_y(ia) = grad.y;
atoms->grad_z(ia) = grad.z;
Expand Down Expand Up @@ -1039,6 +1039,8 @@ void colvar::rmsd::calc_Jacobian_derivative()

// The rotation term only applies is coordinates are rotated
if (atoms->is_enabled(f_ag_rotate)) {
// Use the best symmetry permutation of reference positions
size_t const best_perm_start = atoms->size() * best_perm_index;

// gradient of the rotation matrix
cvm::matrix2d<cvm::rvector> grad_rot_mat(3, 3);
Expand Down Expand Up @@ -1072,7 +1074,7 @@ void colvar::rmsd::calc_Jacobian_derivative()
grad_rot_mat[1][2] = 2.0 * (g23 - g01);
grad_rot_mat[2][2] = -2.0 * (g11 + g22);

cvm::atom_pos &y = ref_pos[ia];
cvm::atom_pos const &y = ref_pos[best_perm_start + ia];

for (size_t alpha = 0; alpha < 3; alpha++) {
for (size_t beta = 0; beta < 3; beta++) {
Expand Down
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