| 57 |
|
// is treated as atom *3* in a standard torsion form: |
| 58 |
|
|
| 59 |
|
Vector3d pos1 = atom2_->getPos(); |
| 60 |
< |
Vector3d pos2 = atom1_->getPos(); |
| 61 |
< |
Vector3d pos3 = atom4_->getPos(); |
| 62 |
< |
Vector3d pos4 = atom3_->getPos(); |
| 60 |
> |
Vector3d pos2 = atom3_->getPos(); |
| 61 |
> |
Vector3d pos3 = atom1_->getPos(); |
| 62 |
> |
Vector3d pos4 = atom4_->getPos(); |
| 63 |
|
|
| 64 |
|
/*std::ofstream myfile; |
| 65 |
|
myfile.open("Inversion", std::ios::app); |
| 69 |
|
<< atom4_->getType() << " - atom4; " |
| 70 |
|
<< std::endl; |
| 71 |
|
*/ |
| 72 |
< |
Vector3d r21 = pos1 - pos2; |
| 73 |
< |
Vector3d r32 = pos2 - pos3; |
| 74 |
< |
Vector3d r42 = pos2 - pos4; |
| 72 |
> |
Vector3d r31 = pos1 - pos3; |
| 73 |
> |
Vector3d r23 = pos3 - pos2; |
| 74 |
> |
Vector3d r43 = pos3 - pos4; |
| 75 |
|
|
| 76 |
|
// Calculate the cross products and distances |
| 77 |
< |
Vector3d A = cross(r21, r32); |
| 77 |
> |
Vector3d A = cross(r31, r43); |
| 78 |
|
RealType rA = A.length(); |
| 79 |
< |
Vector3d B = cross(r32, r42); |
| 79 |
> |
Vector3d B = cross(r43, r23); |
| 80 |
|
RealType rB = B.length(); |
| 81 |
|
//Vector3d C = cross(r23, A); |
| 82 |
|
//RealType rC = C.length(); |
| 103 |
|
Vector3d dcosdA = (cos_phi * A - B) /rA; |
| 104 |
|
Vector3d dcosdB = (cos_phi * B - A) /rB; |
| 105 |
|
|
| 106 |
< |
f1 = dVdcosPhi * cross(r32, dcosdA); |
| 107 |
< |
f2 = dVdcosPhi * ( cross(r42, dcosdB) - cross(r21, dcosdA)); |
| 108 |
< |
f3 = dVdcosPhi * cross(dcosdB, r32); |
| 106 |
> |
f1 = dVdcosPhi * cross(r43, dcosdA); |
| 107 |
> |
f2 = dVdcosPhi * ( cross(r23, dcosdB) - cross(r31, dcosdA)); |
| 108 |
> |
f3 = dVdcosPhi * cross(dcosdB, r43); |
| 109 |
|
|
| 110 |
|
// In OOPSE's version of an improper torsion, the central atom |
| 111 |
|
// comes first. However, to get the planarity in a typical cosine |
