| 35 |
|
* |
| 36 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
|
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
< |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
< |
* [4] Vardeman & Gezelter, in progress (2009). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
#include "restraints/MolecularRestraint.hpp" |
| 71 |
|
|
| 72 |
|
pot_ += p; |
| 73 |
|
|
| 74 |
< |
restInfo_[rtDisplacement] = std::make_pair(r, p); |
| 74 |
> |
if (printRest_) restInfo_[rtDisplacement] = std::make_pair(r, p); |
| 75 |
|
|
| 76 |
|
for(it = forces_.begin(); it != forces_.end(); ++it) |
| 77 |
|
(*it) = -kDisp_ * del * scaleFactor_; |
| 86 |
|
|
| 87 |
|
Mat3x3d R(0.0); |
| 88 |
|
|
| 89 |
< |
for (int n = 0; n < struc.size(); n++){ |
| 89 |
> |
for (unsigned int n = 0; n < struc.size(); n++){ |
| 90 |
|
|
| 91 |
|
/* |
| 92 |
|
* correlation matrix R: |
| 138 |
|
Vector3d eularAngles = A.toEulerAngles(); |
| 139 |
|
|
| 140 |
|
|
| 141 |
< |
RealType twistAngle, swingAngle; |
| 141 |
> |
RealType twistAngle; |
| 142 |
|
Vector3d swingAxis; |
| 143 |
|
|
| 144 |
|
Quat4d quat = A.toQuaternion(); |
| 145 |
|
|
| 146 |
< |
RealType tw, sx, sy, ttw, swingX, swingY; |
| 146 |
> |
RealType swingX, swingY; |
| 147 |
|
quat.toSwingTwist(swingX, swingY, twistAngle); |
| 148 |
|
|
| 149 |
< |
RealType dVdtwist, dVdswing, dVdswingX, dVdswingY; |
| 150 |
< |
RealType dTwist, dSwing, dSwingX, dSwingY; |
| 149 |
> |
RealType dVdtwist, dVdswingX, dVdswingY; |
| 150 |
> |
RealType dTwist, dSwingX, dSwingY; |
| 151 |
|
RealType p; |
| 152 |
|
|
| 153 |
|
if (restType_ & rtTwist){ |
| 154 |
|
dTwist = twistAngle - twist0_; |
| 155 |
< |
dVdtwist = kTwist_ * sin(dTwist) ; |
| 156 |
< |
p = kTwist_ * (1.0 - cos(dTwist) ) ; |
| 155 |
> |
/// dVdtwist = kTwist_ * sin(dTwist) ; |
| 156 |
> |
/// p = kTwist_ * (1.0 - cos(dTwist) ) ; |
| 157 |
> |
dVdtwist = kTwist_ * dTwist; |
| 158 |
> |
p = 0.5 * kTwist_ * dTwist * dTwist; |
| 159 |
|
pot_ += p; |
| 160 |
|
tBody -= dVdtwist * V3Z; |
| 161 |
< |
restInfo_[rtTwist] = std::make_pair(twistAngle, p); |
| 161 |
> |
if (printRest_) restInfo_[rtTwist] = std::make_pair(twistAngle, p); |
| 162 |
|
} |
| 163 |
|
|
| 161 |
– |
// if (restType_ & rtSwing){ |
| 162 |
– |
// dSwing = swingAngle - swing0_; |
| 163 |
– |
// dVdswing = kSwing_ * 2.0 * sin(2.0 * dSwing); |
| 164 |
– |
// p = kSwing_ * (1.0 - cos(2.0 * dSwing)); |
| 165 |
– |
// pot_ += p; |
| 166 |
– |
// tBody -= dVdswing * swingAxis; |
| 167 |
– |
// restInfo_[rtSwing] = std::make_pair(swingAngle, p); |
| 168 |
– |
// } |
| 169 |
– |
|
| 164 |
|
if (restType_ & rtSwingX){ |
| 165 |
|
dSwingX = swingX - swingX0_; |
| 166 |
< |
dVdswingX = kSwingX_ * 2.0 * sin(2.0 * dSwingX); |
| 167 |
< |
p = kSwingX_ * (1.0 - cos(2.0 * dSwingX)); |
| 166 |
> |
/// dVdswingX = kSwingX_ * 2.0 * sin(2.0 * dSwingX); |
| 167 |
> |
/// p = kSwingX_ * (1.0 - cos(2.0 * dSwingX)); |
| 168 |
> |
dVdswingX = kSwingX_ * dSwingX; |
| 169 |
> |
p = 0.5 * kSwingX_ * dSwingX * dSwingX; |
| 170 |
|
pot_ += p; |
| 171 |
|
tBody -= dVdswingX * V3X; |
| 172 |
< |
restInfo_[rtSwingX] = std::make_pair(swingX, p); |
| 172 |
> |
if (printRest_) restInfo_[rtSwingX] = std::make_pair(swingX, p); |
| 173 |
|
} |
| 174 |
|
if (restType_ & rtSwingY){ |
| 175 |
|
dSwingY = swingY - swingY0_; |
| 176 |
< |
dVdswingY = kSwingY_ * 2.0 * sin(2.0 * dSwingY); |
| 177 |
< |
p = kSwingY_ * (1.0 - cos(2.0 * dSwingY)); |
| 176 |
> |
/// dVdswingY = kSwingY_ * 2.0 * sin(2.0 * dSwingY); |
| 177 |
> |
/// p = kSwingY_ * (1.0 - cos(2.0 * dSwingY)); |
| 178 |
> |
dVdswingY = kSwingY_ * dSwingY; |
| 179 |
> |
p = 0.5 * kSwingX_ * dSwingY * dSwingY; |
| 180 |
|
pot_ += p; |
| 181 |
|
tBody -= dVdswingY * V3Y; |
| 182 |
< |
restInfo_[rtSwingY] = std::make_pair(swingY, p); |
| 182 |
> |
if (printRest_) restInfo_[rtSwingY] = std::make_pair(swingY, p); |
| 183 |
|
} |
| 184 |
|
|
| 185 |
|
|
| 187 |
|
|
| 188 |
|
Vector3d rLab, rBody, txr, fBody, fLab; |
| 189 |
|
|
| 190 |
< |
for (int i = 0; i < struc.size(); i++) { |
| 190 |
> |
for (unsigned int i = 0; i < struc.size(); i++) { |
| 191 |
|
|
| 192 |
|
rLab = struc[i]; |
| 193 |
|
rBody = A * rLab; |
