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Commit bbe0ce70 authored by peastman's avatar peastman
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Fixed incorrect specification of torsion-torsion terms in AMOEBA 2013 force field

parent 25e3852a
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Showing with 1903 additions and 15 deletions
plugins/amoeba/openmmapi/src/AmoebaTorsionTorsionForce.cpp
View file @ bbe0ce70
...@@ -86,42 +86,55 @@ ForceImpl* AmoebaTorsionTorsionForce::createImpl() const { ...@@ -86,42 +86,55 @@ ForceImpl* AmoebaTorsionTorsionForce::createImpl() const {
} }
AmoebaTorsionTorsionForce::TorsionTorsionGridInfo::TorsionTorsionGridInfo(const TorsionTorsionGrid& grid) { AmoebaTorsionTorsionForce::TorsionTorsionGridInfo::TorsionTorsionGridInfo(const TorsionTorsionGrid& grid) {
if (grid[0][0][0] != grid[1][0][0])
_grid = grid; _grid = grid;
else {
// We need to transpose the grid.
int xsize = grid[0].size();
int ysize = grid.size();
_grid.resize(xsize);
for (int i = 0; i < xsize; i++) {
_grid[i].resize(ysize);
for (int j = 0; j < ysize; j++)
_grid[i][j] = grid[j][i];
}
}
_startValues[0] = _grid[0][0][0]; _startValues[0] = _grid[0][0][0];
_startValues[1] = _grid[0][0][1]; _startValues[1] = _grid[0][0][1];
_spacing[0] = static_cast<double>(_grid.size()-1)/360.0; _spacing[0] = static_cast<double>(_grid.size()-1)/360.0;
_spacing[1] = static_cast<double>(grid.size()-1)/360.0; _spacing[1] = static_cast<double>(_grid.size()-1)/360.0;
_size[0] = static_cast<int>(grid.size()); _size[0] = static_cast<int>(_grid.size());
_size[1] = static_cast<int>(grid[0].size()); _size[1] = static_cast<int>(_grid[0].size());
if (grid[0][0].size() == 3) { if (_grid[0][0].size() == 3) {
// We need to compute the derivatives ourselves. First determine if the grid is periodic. // We need to compute the derivatives ourselves. First determine if the grid is periodic.
int xsize = _size[0]; int xsize = _size[0];
int ysize = _size[1]; int ysize = _size[1];
bool periodic = true; bool periodic = true;
for (int i = 0; i < xsize; i++) for (int i = 0; i < xsize; i++)
if (grid[i][0][2] != grid[i][ysize-1][2]) if (_grid[i][0][2] != _grid[i][ysize-1][2])
periodic = false; periodic = false;
for (int i = 0; i < ysize; i++) for (int i = 0; i < ysize; i++)
if (grid[0][i][2] != grid[xsize-1][i][2]) if (_grid[0][i][2] != _grid[xsize-1][i][2])
periodic = false; periodic = false;
// Compute derivatives with respect to the first angle. // Compute derivatives with respect to the first angle.
vector<double> x(xsize), y(ysize); vector<double> x(xsize), y(ysize);
for (int i = 0; i < xsize; i++) for (int i = 0; i < xsize; i++)
x[i] = grid[i][0][0]; x[i] = _grid[i][0][0];
for (int i = 0; i < xsize; i++) for (int i = 0; i < ysize; i++)
y[i] = grid[0][i][1]; y[i] = _grid[0][i][1];
vector<double> d1(xsize*ysize), d2(xsize*ysize), d12(xsize*ysize); vector<double> d1(xsize*ysize), d2(xsize*ysize), d12(xsize*ysize);
vector<double> t(xsize), deriv(xsize); vector<double> t(xsize), deriv(xsize);
for (int i = 0; i < ysize; i++) { for (int i = 0; i < ysize; i++) {
for (int j = 0; j < xsize; j++) for (int j = 0; j < xsize; j++)
t[j] = grid[j][i][2]; t[j] = _grid[j][i][2];
if (periodic) if (periodic)
SplineFitter::createPeriodicSpline(x, t, deriv); SplineFitter::createPeriodicSpline(x, t, deriv);
else else
...@@ -136,7 +149,7 @@ AmoebaTorsionTorsionForce::TorsionTorsionGridInfo::TorsionTorsionGridInfo(const ...@@ -136,7 +149,7 @@ AmoebaTorsionTorsionForce::TorsionTorsionGridInfo::TorsionTorsionGridInfo(const
deriv.resize(ysize); deriv.resize(ysize);
for (int i = 0; i < xsize; i++) { for (int i = 0; i < xsize; i++) {
for (int j = 0; j < ysize; j++) for (int j = 0; j < ysize; j++)
t[j] = grid[i][j][2]; t[j] = _grid[i][j][2];
if (periodic) if (periodic)
SplineFitter::createPeriodicSpline(y, t, deriv); SplineFitter::createPeriodicSpline(y, t, deriv);
else else
......
wrappers/python/simtk/openmm/app/data/amoeba2013.xml
View file @ bbe0ce70
<ForceField> <ForceField>
<Info> <Info>
<Source>amoebapro13.prm</Source> <Source>amoebapro13.prm</Source>
<DateGenerated>2014-03-11</DateGenerated> <DateGenerated>2014-05-08</DateGenerated>
<Reference>Yue Shi, Zhen Xia, Jiajing Zhang, Robert Best, Chuanjie Wu, Jay W. Ponder, and Pengyu Ren. Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins. Journal of Chemical Theory and Computation, 9(9):4046–4063, 2013.</Reference> <Reference>Yue Shi, Zhen Xia, Jiajing Zhang, Robert Best, Chuanjie Wu, Jay W. Ponder, and Pengyu Ren. Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins. Journal of Chemical Theory and Computation, 9(9):4046–4063, 2013.</Reference>
</Info> </Info>
<AtomTypes> <AtomTypes>
...@@ -4273,10 +4273,1885 @@ ...@@ -4273,10 +4273,1885 @@
<TorsionTorsion class1="3" class2="1" class3="2" class4="32" class5="34" grid="1" nx="25" ny="25" /> <TorsionTorsion class1="3" class2="1" class3="2" class4="32" class5="34" grid="1" nx="25" ny="25" />
<TorsionTorsion class1="3" class2="1" class3="2" class4="3" class5="15" grid="2" nx="25" ny="25" /> <TorsionTorsion class1="3" class2="1" class3="2" class4="3" class5="15" grid="2" nx="25" ny="25" />
<TorsionTorsionGrid grid="0" nx="25" ny="25" > <TorsionTorsionGrid grid="0" nx="25" ny="25" >
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<Grid angle1="165.0" angle2="180.0" f="-2.83876032" />
<Grid angle1="180.0" angle2="180.0" f="-1.7166952" />
</TorsionTorsionGrid > </TorsionTorsionGrid >
</AmoebaTorsionTorsionForce> </AmoebaTorsionTorsionForce>
<AmoebaVdwForce type="BUFFERED-14-7" radiusrule="CUBIC-MEAN" radiustype="R-MIN" radiussize="DIAMETER" epsilonrule="HHG" vdw-13-scale="0.0" vdw-14-scale="1.0" vdw-15-scale="1.0" > <AmoebaVdwForce type="BUFFERED-14-7" radiusrule="CUBIC-MEAN" radiustype="R-MIN" radiussize="DIAMETER" epsilonrule="HHG" vdw-13-scale="0.0" vdw-14-scale="1.0" vdw-15-scale="1.0" >
......
wrappers/python/simtk/openmm/app/data/amoeba2013_gk.xml
View file @ bbe0ce70
<ForceField> <ForceField>
<Info> <Info>
<Source>amoebapro13.prm</Source> <Source>amoebapro13.prm</Source>
<DateGenerated>2014-03-11</DateGenerated> <DateGenerated>2014-05-08</DateGenerated>
<Reference>Yue Shi, Zhen Xia, Jiajing Zhang, Robert Best, Chuanjie Wu, Jay W. Ponder, and Pengyu Ren. Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins. Journal of Chemical Theory and Computation, 9(9):4046–4063, 2013.</Reference> <Reference>Yue Shi, Zhen Xia, Jiajing Zhang, Robert Best, Chuanjie Wu, Jay W. Ponder, and Pengyu Ren. Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins. Journal of Chemical Theory and Computation, 9(9):4046–4063, 2013.</Reference>
</Info> </Info>
<AmoebaGeneralizedKirkwoodForce solventDielectric="78.3" soluteDielectric="1.0" includeCavityTerm="1" probeRadius="0.14" surfaceAreaFactor="-170.351730663"> <AmoebaGeneralizedKirkwoodForce solventDielectric="78.3" soluteDielectric="1.0" includeCavityTerm="1" probeRadius="0.14" surfaceAreaFactor="-170.351730663">
......
wrappers/python/simtk/openmm/app/forcefield.py
View file @ bbe0ce70
...@@ -2505,7 +2505,7 @@ class AmoebaTorsionTorsionGenerator: ...@@ -2505,7 +2505,7 @@ class AmoebaTorsionTorsionGenerator:
gridRow.append(float(gridEntry.attrib['angle1'])) gridRow.append(float(gridEntry.attrib['angle1']))
gridRow.append(float(gridEntry.attrib['angle2'])) gridRow.append(float(gridEntry.attrib['angle2']))
gridRow.append(float(gridEntry.attrib['f'])) gridRow.append(float(gridEntry.attrib['f']))
if 'fx' in gridEnergy.attrib: if 'fx' in gridEntry.attrib:
gridRow.append(float(gridEntry.attrib['fx'])) gridRow.append(float(gridEntry.attrib['fx']))
gridRow.append(float(gridEntry.attrib['fy'])) gridRow.append(float(gridEntry.attrib['fy']))
gridRow.append(float(gridEntry.attrib['fxy'])) gridRow.append(float(gridEntry.attrib['fxy']))
......
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