Skip to content

GitLab

Commit 46479322 authored by peastman's avatar peastman
Browse files

Merge pull request #531 from peastman/charmm 

Implemented CHARMM polarizable force field
parents 56f9f6f6 9128e9ef
Hide whitespace changes
Inline Side-by-side
Showing with 11561 additions and 139 deletions
docs/usersguide/application.rst
View file @ 46479322
...@@ -651,19 +651,20 @@ For the main force field, OpenMM provides the following options: ...@@ -651,19 +651,20 @@ For the main force field, OpenMM provides the following options:
.. tabularcolumns:: |l|L| .. tabularcolumns:: |l|L|
================= ================================================================================ ===================== ================================================================================
File Force Field File Force Field
================= ================================================================================ ===================== ================================================================================
amber96.xml AMBER96\ :cite:`Kollman1997` amber96.xml AMBER96\ :cite:`Kollman1997`
amber99sb.xml AMBER99\ :cite:`Wang2000` with modified backbone torsions\ :cite:`Hornak2006` amber99sb.xml AMBER99\ :cite:`Wang2000` with modified backbone torsions\ :cite:`Hornak2006`
amber99sbildn.xml AMBER99SB plus improved side chain torsions\ :cite:`Lindorff-Larsen2010` amber99sbildn.xml AMBER99SB plus improved side chain torsions\ :cite:`Lindorff-Larsen2010`
amber99sbnmr.xml AMBER99SB with modifications to fit NMR data\ :cite:`Li2010` amber99sbnmr.xml AMBER99SB with modifications to fit NMR data\ :cite:`Li2010`
amber03.xml AMBER03\ :cite:`Duan2003` amber03.xml AMBER03\ :cite:`Duan2003`
amber10.xml AMBER10 amber10.xml AMBER10
amoeba2009.xml AMOEBA 2009\ :cite:`Ren2002`. This force field is deprecated. It is amoeba2009.xml AMOEBA 2009\ :cite:`Ren2002`. This force field is deprecated. It is
recommended to use AMOEBA 2013 instead. recommended to use AMOEBA 2013 instead.
amoeba2013.xml AMOEBA 2013\ :cite:`Shi2013` amoeba2013.xml AMOEBA 2013\ :cite:`Shi2013`
================= ================================================================================ charmm_polar_2013.xml CHARMM 2013 polarizable force field\ :cite:`Lopes2013`
===================== ================================================================================
The AMBER files do not include parameters for water molecules. This allows you The AMBER files do not include parameters for water molecules. This allows you
...@@ -686,10 +687,10 @@ swm4ndp.xml SWM4-NDP water model\ :cite:`Lamoureux2006` ...@@ -686,10 +687,10 @@ swm4ndp.xml SWM4-NDP water model\ :cite:`Lamoureux2006`
=========== ============================================ =========== ============================================
For the AMOEBA force field, only one explicit water model is currently available For the polarizable force fields (AMOEBA and CHARMM), only one explicit water model
and the water parameters are included in the file :code:`amoeba2009.xml`\ . is currently available and the water parameters are included in the same file as
Also the AMOEBA force field file only includes the parameters for amino acids the macromolecule parameters. Also, the polarizable force fields only include
and ions; nucleic acids will be included in a future release. parameters for amino acids and ions, not for nucleic acids.
If you want to include an implicit solvation model, you can also specify one of If you want to include an implicit solvation model, you can also specify one of
the following files: the following files:
......
docs/usersguide/references.bib
View file @ 46479322
...@@ -215,6 +215,17 @@ ...@@ -215,6 +215,17 @@
type = {Journal Article} type = {Journal Article}
} }
@article{Lopes2013,
author = {Lopes, Pedro E. M. and Huang, Jing and Shim, Jihyun and Luo, Yun and Li, Hui and Roux, Benoît and MacKerell, Alexander D.},
title = {Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator},
journal = {Journal of Chemical Theory and Computation},
volume = {9},
number = {12},
pages = {5430-5449},
year = {2013},
type = {Journal Article}
}
@article{Mahoney2000 @article{Mahoney2000
author = {Mahoney, Michael W. and Jorgensen, William L.}, author = {Mahoney, Michael W. and Jorgensen, William L.},
title = {A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions}, title = {A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions},
......
plugins/drude/platforms/cuda/src/CudaDrudeKernels.cpp
View file @ 46479322
...@@ -126,9 +126,9 @@ void CudaCalcDrudeForceKernel::initialize(const System& system, const DrudeForce ...@@ -126,9 +126,9 @@ void CudaCalcDrudeForceKernel::initialize(const System& system, const DrudeForce
double a1 = (atoms[i][2] == -1 ? 1 : aniso12); double a1 = (atoms[i][2] == -1 ? 1 : aniso12);
double a2 = (atoms[i][3] == -1 || atoms[i][4] == -1 ? 1 : aniso34); double a2 = (atoms[i][3] == -1 || atoms[i][4] == -1 ? 1 : aniso34);
double a3 = 3-a1-a2; double a3 = 3-a1-a2;
double k3 = charge*charge/(polarizability*a3); double k3 = ONE_4PI_EPS0*charge*charge/(polarizability*a3);
double k1 = charge*charge/(polarizability*a1) - k3; double k1 = ONE_4PI_EPS0*charge*charge/(polarizability*a1) - k3;
double k2 = charge*charge/(polarizability*a2) - k3; double k2 = ONE_4PI_EPS0*charge*charge/(polarizability*a2) - k3;
if (atoms[i][2] == -1) { if (atoms[i][2] == -1) {
atoms[i][2] = 0; atoms[i][2] = 0;
k1 = 0; k1 = 0;
......
plugins/drude/platforms/cuda/src/kernels/drudePairForce.cu
View file @ 46479322
...@@ -13,7 +13,7 @@ real u = drudeParams.x*r; ...@@ -13,7 +13,7 @@ real u = drudeParams.x*r;
real screening = 1-(1+0.5f*u)*EXP(-u); real screening = 1-(1+0.5f*u)*EXP(-u);
real pairEnergy = drudeParams.y*screening*rInv; real pairEnergy = drudeParams.y*screening*rInv;
energy += pairEnergy; energy += pairEnergy;
real3 f = delta*(pairEnergy*rInv*rInv); real3 f = delta*(drudeParams.y*rInv*rInv*(screening*rInv-0.5f*(1+u)*EXP(-u)*drudeParams.x));
force1 += f; force1 += f;
force3 -= f; force3 -= f;
...@@ -26,7 +26,7 @@ u = drudeParams.x*r; ...@@ -26,7 +26,7 @@ u = drudeParams.x*r;
screening = 1-(1+0.5f*u)*EXP(-u); screening = 1-(1+0.5f*u)*EXP(-u);
pairEnergy = -drudeParams.y*screening*rInv; pairEnergy = -drudeParams.y*screening*rInv;
energy += pairEnergy; energy += pairEnergy;
f = delta*(pairEnergy*rInv*rInv); f = delta*(-drudeParams.y*rInv*rInv*(screening*rInv-0.5f*(1+u)*EXP(-u)*drudeParams.x));
force1 += f; force1 += f;
force4 -= f; force4 -= f;
...@@ -39,7 +39,7 @@ u = drudeParams.x*r; ...@@ -39,7 +39,7 @@ u = drudeParams.x*r;
screening = 1-(1+0.5f*u)*EXP(-u); screening = 1-(1+0.5f*u)*EXP(-u);
pairEnergy = -drudeParams.y*screening*rInv; pairEnergy = -drudeParams.y*screening*rInv;
energy += pairEnergy; energy += pairEnergy;
f = delta*(pairEnergy*rInv*rInv); f = delta*(-drudeParams.y*rInv*rInv*(screening*rInv-0.5f*(1+u)*EXP(-u)*drudeParams.x));
force2 += f; force2 += f;
force3 -= f; force3 -= f;
...@@ -52,6 +52,6 @@ u = drudeParams.x*r; ...@@ -52,6 +52,6 @@ u = drudeParams.x*r;
screening = 1-(1+0.5f*u)*EXP(-u); screening = 1-(1+0.5f*u)*EXP(-u);
pairEnergy = drudeParams.y*screening*rInv; pairEnergy = drudeParams.y*screening*rInv;
energy += pairEnergy; energy += pairEnergy;
f = delta*(pairEnergy*rInv*rInv); f = delta*(drudeParams.y*rInv*rInv*(screening*rInv-0.5f*(1+u)*EXP(-u)*drudeParams.x));
force2 += f; force2 += f;
force4 -= f; force4 -= f;
plugins/drude/platforms/cuda/tests/TestCudaDrudeForce.cpp
View file @ 46479322
...@@ -76,9 +76,9 @@ void validateForce(System& system, vector<Vec3>& positions, double expectedEnerg ...@@ -76,9 +76,9 @@ void validateForce(System& system, vector<Vec3>& positions, double expectedEnerg
} }
void testSingleParticle() { void testSingleParticle() {
const double k = 1.5; const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1; const double charge = 0.1;
const double alpha = charge*charge/k; const double alpha = ONE_4PI_EPS0*charge*charge/k;
System system; System system;
system.addParticle(1.0); system.addParticle(1.0);
system.addParticle(1.0); system.addParticle(1.0);
...@@ -92,9 +92,9 @@ void testSingleParticle() { ...@@ -92,9 +92,9 @@ void testSingleParticle() {
} }
void testAnisotropicParticle() { void testAnisotropicParticle() {
const double k = 1.5; const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1; const double charge = 0.1;
const double alpha = charge*charge/k; const double alpha = ONE_4PI_EPS0*charge*charge/k;
const double a1 = 0.8; const double a1 = 0.8;
const double a2 = 1.1; const double a2 = 1.1;
const double k1 = k/a1; const double k1 = k/a1;
...@@ -124,9 +124,9 @@ double computeScreening(double r, double thole, double alpha1, double alpha2) { ...@@ -124,9 +124,9 @@ double computeScreening(double r, double thole, double alpha1, double alpha2) {
} }
void testThole() { void testThole() {
const double k = 1.5; const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1; const double charge = 0.1;
const double alpha = charge*charge/k; const double alpha = ONE_4PI_EPS0*charge*charge/k;
const double thole = 2.5; const double thole = 2.5;
System system; System system;
system.addParticle(1.0); system.addParticle(1.0);
...@@ -157,9 +157,9 @@ void testThole() { ...@@ -157,9 +157,9 @@ void testThole() {
} }
void testChangingParameters() { void testChangingParameters() {
const double k = 1.5; const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1; const double charge = 0.1;
const double alpha = charge*charge/k; const double alpha = ONE_4PI_EPS0*charge*charge/k;
Platform& platform = Platform::getPlatformByName("CUDA"); Platform& platform = Platform::getPlatformByName("CUDA");
// Create the system. // Create the system.
...@@ -184,9 +184,9 @@ void testChangingParameters() { ...@@ -184,9 +184,9 @@ void testChangingParameters() {
// Modify the parameters. // Modify the parameters.
const double k2 = 2.2; const double k2 = ONE_4PI_EPS0*2.2;
const double charge2 = 0.3; const double charge2 = 0.3;
const double alpha2 = charge2*charge2/k2; const double alpha2 = ONE_4PI_EPS0*charge2*charge2/k2;
drude->setParticleParameters(0, 1, 0, -1, -1, -1, charge2, alpha2, 1, 1); drude->setParticleParameters(0, 1, 0, -1, -1, -1, charge2, alpha2, 1, 1);
drude->updateParametersInContext(context); drude->updateParametersInContext(context);
state = context.getState(State::Energy); state = context.getState(State::Energy);
......
plugins/drude/platforms/cuda/tests/TestCudaDrudeLangevinIntegrator.cpp
View file @ 46479322
...@@ -53,9 +53,9 @@ extern "C" OPENMM_EXPORT void registerDrudeCudaKernelFactories(); ...@@ -53,9 +53,9 @@ extern "C" OPENMM_EXPORT void registerDrudeCudaKernelFactories();
void testSinglePair() { void testSinglePair() {
const double temperature = 300.0; const double temperature = 300.0;
const double temperatureDrude = 10.0; const double temperatureDrude = 10.0;
const double k = 1.5; const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1; const double charge = 0.1;
const double alpha = charge*charge/k; const double alpha = ONE_4PI_EPS0*charge*charge/k;
const double mass1 = 1.0; const double mass1 = 1.0;
const double mass2 = 0.1; const double mass2 = 0.1;
const double totalMass = mass1+mass2; const double totalMass = mass1+mass2;
...@@ -132,7 +132,7 @@ void testWater() { ...@@ -132,7 +132,7 @@ void testWater() {
system.addConstraint(startIndex, startIndex+3, 0.09572); system.addConstraint(startIndex, startIndex+3, 0.09572);
system.addConstraint(startIndex+2, startIndex+3, 0.15139); system.addConstraint(startIndex+2, startIndex+3, 0.15139);
system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721)); system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721));
drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, 1.71636*1.71636/(100000*4.184), 1, 1); drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, ONE_4PI_EPS0*1.71636*1.71636/(100000*4.184), 1, 1);
} }
vector<Vec3> positions; vector<Vec3> positions;
for (int i = 0; i < gridSize; i++) for (int i = 0; i < gridSize; i++)
......
plugins/drude/platforms/cuda/tests/TestCudaDrudeSCFIntegrator.cpp
View file @ 46479322
...@@ -85,7 +85,7 @@ void testWater() { ...@@ -85,7 +85,7 @@ void testWater() {
system.addConstraint(startIndex, startIndex+3, 0.09572); system.addConstraint(startIndex, startIndex+3, 0.09572);
system.addConstraint(startIndex+2, startIndex+3, 0.15139); system.addConstraint(startIndex+2, startIndex+3, 0.15139);
system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721)); system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721));
drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, 1.71636*1.71636/(100000*4.184), 1, 1); drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, ONE_4PI_EPS0*1.71636*1.71636/(100000*4.184), 1, 1);
} }
vector<Vec3> positions; vector<Vec3> positions;
for (int i = 0; i < gridSize; i++) for (int i = 0; i < gridSize; i++)
......
plugins/drude/platforms/opencl/src/OpenCLDrudeKernels.cpp
View file @ 46479322
...@@ -131,9 +131,9 @@ void OpenCLCalcDrudeForceKernel::initialize(const System& system, const DrudeFor ...@@ -131,9 +131,9 @@ void OpenCLCalcDrudeForceKernel::initialize(const System& system, const DrudeFor
double a1 = (atoms[i][2] == -1 ? 1 : aniso12); double a1 = (atoms[i][2] == -1 ? 1 : aniso12);
double a2 = (atoms[i][3] == -1 || atoms[i][4] == -1 ? 1 : aniso34); double a2 = (atoms[i][3] == -1 || atoms[i][4] == -1 ? 1 : aniso34);
double a3 = 3-a1-a2; double a3 = 3-a1-a2;
double k3 = charge*charge/(polarizability*a3); double k3 = ONE_4PI_EPS0*charge*charge/(polarizability*a3);
double k1 = charge*charge/(polarizability*a1) - k3; double k1 = ONE_4PI_EPS0*charge*charge/(polarizability*a1) - k3;
double k2 = charge*charge/(polarizability*a2) - k3; double k2 = ONE_4PI_EPS0*charge*charge/(polarizability*a2) - k3;
if (atoms[i][2] == -1) { if (atoms[i][2] == -1) {
atoms[i][2] = 0; atoms[i][2] = 0;
k1 = 0; k1 = 0;
......
plugins/drude/platforms/opencl/src/kernels/drudePairForce.cl
View file @ 46479322
...@@ -13,7 +13,7 @@ real u = drudeParams.x*r; ...@@ -13,7 +13,7 @@ real u = drudeParams.x*r;
real screening = 1-(1+0.5f*u)*EXP(-u); real screening = 1-(1+0.5f*u)*EXP(-u);
real pairEnergy = drudeParams.y*screening*rInv; real pairEnergy = drudeParams.y*screening*rInv;
energy += pairEnergy; energy += pairEnergy;
real4 f = delta*(pairEnergy*rInv*rInv); real4 f = delta*(drudeParams.y*rInv*rInv)*(screening*rInv-0.5f*(1+u)*EXP(-u)*drudeParams.x);
force1 += f; force1 += f;
force3 -= f; force3 -= f;
...@@ -26,7 +26,7 @@ u = drudeParams.x*r; ...@@ -26,7 +26,7 @@ u = drudeParams.x*r;
screening = 1-(1+0.5f*u)*EXP(-u); screening = 1-(1+0.5f*u)*EXP(-u);
pairEnergy = -drudeParams.y*screening*rInv; pairEnergy = -drudeParams.y*screening*rInv;
energy += pairEnergy; energy += pairEnergy;
f = delta*(pairEnergy*rInv*rInv); f = delta*(-drudeParams.y*rInv*rInv)*(screening*rInv-0.5f*(1+u)*EXP(-u)*drudeParams.x);
force1 += f; force1 += f;
force4 -= f; force4 -= f;
...@@ -39,7 +39,7 @@ u = drudeParams.x*r; ...@@ -39,7 +39,7 @@ u = drudeParams.x*r;
screening = 1-(1+0.5f*u)*EXP(-u); screening = 1-(1+0.5f*u)*EXP(-u);
pairEnergy = -drudeParams.y*screening*rInv; pairEnergy = -drudeParams.y*screening*rInv;
energy += pairEnergy; energy += pairEnergy;
f = delta*(pairEnergy*rInv*rInv); f = delta*(-drudeParams.y*rInv*rInv)*(screening*rInv-0.5f*(1+u)*EXP(-u)*drudeParams.x);
force2 += f; force2 += f;
force3 -= f; force3 -= f;
...@@ -52,6 +52,6 @@ u = drudeParams.x*r; ...@@ -52,6 +52,6 @@ u = drudeParams.x*r;
screening = 1-(1+0.5f*u)*EXP(-u); screening = 1-(1+0.5f*u)*EXP(-u);
pairEnergy = drudeParams.y*screening*rInv; pairEnergy = drudeParams.y*screening*rInv;
energy += pairEnergy; energy += pairEnergy;
f = delta*(pairEnergy*rInv*rInv); f = delta*(drudeParams.y*rInv*rInv)*(screening*rInv-0.5f*(1+u)*EXP(-u)*drudeParams.x);
force2 += f; force2 += f;
force4 -= f; force4 -= f;
plugins/drude/platforms/opencl/tests/TestOpenCLDrudeForce.cpp
View file @ 46479322
...@@ -76,9 +76,9 @@ void validateForce(System& system, vector<Vec3>& positions, double expectedEnerg ...@@ -76,9 +76,9 @@ void validateForce(System& system, vector<Vec3>& positions, double expectedEnerg
} }
void testSingleParticle() { void testSingleParticle() {
const double k = 1.5; const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1; const double charge = 0.1;
const double alpha = charge*charge/k; const double alpha = ONE_4PI_EPS0*charge*charge/k;
System system; System system;
system.addParticle(1.0); system.addParticle(1.0);
system.addParticle(1.0); system.addParticle(1.0);
...@@ -92,9 +92,9 @@ void testSingleParticle() { ...@@ -92,9 +92,9 @@ void testSingleParticle() {
} }
void testAnisotropicParticle() { void testAnisotropicParticle() {
const double k = 1.5; const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1; const double charge = 0.1;
const double alpha = charge*charge/k; const double alpha = ONE_4PI_EPS0*charge*charge/k;
const double a1 = 0.8; const double a1 = 0.8;
const double a2 = 1.1; const double a2 = 1.1;
const double k1 = k/a1; const double k1 = k/a1;
...@@ -124,9 +124,9 @@ double computeScreening(double r, double thole, double alpha1, double alpha2) { ...@@ -124,9 +124,9 @@ double computeScreening(double r, double thole, double alpha1, double alpha2) {
} }
void testThole() { void testThole() {
const double k = 1.5; const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1; const double charge = 0.1;
const double alpha = charge*charge/k; const double alpha = ONE_4PI_EPS0*charge*charge/k;
const double thole = 2.5; const double thole = 2.5;
System system; System system;
system.addParticle(1.0); system.addParticle(1.0);
...@@ -157,9 +157,9 @@ void testThole() { ...@@ -157,9 +157,9 @@ void testThole() {
} }
void testChangingParameters() { void testChangingParameters() {
const double k = 1.5; const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1; const double charge = 0.1;
const double alpha = charge*charge/k; const double alpha = ONE_4PI_EPS0*charge*charge/k;
Platform& platform = Platform::getPlatformByName("OpenCL"); Platform& platform = Platform::getPlatformByName("OpenCL");
// Create the system. // Create the system.
...@@ -184,9 +184,9 @@ void testChangingParameters() { ...@@ -184,9 +184,9 @@ void testChangingParameters() {
// Modify the parameters. // Modify the parameters.
const double k2 = 2.2; const double k2 = ONE_4PI_EPS0*2.2;
const double charge2 = 0.3; const double charge2 = 0.3;
const double alpha2 = charge2*charge2/k2; const double alpha2 = ONE_4PI_EPS0*charge2*charge2/k2;
drude->setParticleParameters(0, 1, 0, -1, -1, -1, charge2, alpha2, 1, 1); drude->setParticleParameters(0, 1, 0, -1, -1, -1, charge2, alpha2, 1, 1);
drude->updateParametersInContext(context); drude->updateParametersInContext(context);
state = context.getState(State::Energy); state = context.getState(State::Energy);
......
plugins/drude/platforms/opencl/tests/TestOpenCLDrudeLangevinIntegrator.cpp
View file @ 46479322
...@@ -53,9 +53,9 @@ extern "C" OPENMM_EXPORT void registerDrudeOpenCLKernelFactories(); ...@@ -53,9 +53,9 @@ extern "C" OPENMM_EXPORT void registerDrudeOpenCLKernelFactories();
void testSinglePair() { void testSinglePair() {
const double temperature = 300.0; const double temperature = 300.0;
const double temperatureDrude = 10.0; const double temperatureDrude = 10.0;
const double k = 1.5; const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1; const double charge = 0.1;
const double alpha = charge*charge/k; const double alpha = ONE_4PI_EPS0*charge*charge/k;
const double mass1 = 1.0; const double mass1 = 1.0;
const double mass2 = 0.1; const double mass2 = 0.1;
const double totalMass = mass1+mass2; const double totalMass = mass1+mass2;
...@@ -132,7 +132,7 @@ void testWater() { ...@@ -132,7 +132,7 @@ void testWater() {
system.addConstraint(startIndex, startIndex+3, 0.09572); system.addConstraint(startIndex, startIndex+3, 0.09572);
system.addConstraint(startIndex+2, startIndex+3, 0.15139); system.addConstraint(startIndex+2, startIndex+3, 0.15139);
system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721)); system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721));
drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, 1.71636*1.71636/(100000*4.184), 1, 1); drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, ONE_4PI_EPS0*1.71636*1.71636/(100000*4.184), 1, 1);
} }
vector<Vec3> positions; vector<Vec3> positions;
for (int i = 0; i < gridSize; i++) for (int i = 0; i < gridSize; i++)
......
plugins/drude/platforms/opencl/tests/TestOpenCLDrudeSCFIntegrator.cpp
View file @ 46479322
...@@ -85,7 +85,7 @@ void testWater() { ...@@ -85,7 +85,7 @@ void testWater() {
system.addConstraint(startIndex, startIndex+3, 0.09572); system.addConstraint(startIndex, startIndex+3, 0.09572);
system.addConstraint(startIndex+2, startIndex+3, 0.15139); system.addConstraint(startIndex+2, startIndex+3, 0.15139);
system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721)); system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721));
drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, 1.71636*1.71636/(100000*4.184), 1, 1); drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, ONE_4PI_EPS0*1.71636*1.71636/(100000*4.184), 1, 1);
} }
vector<Vec3> positions; vector<Vec3> positions;
for (int i = 0; i < gridSize; i++) for (int i = 0; i < gridSize; i++)
......
plugins/drude/platforms/reference/src/ReferenceDrudeKernels.cpp
View file @ 46479322
...@@ -6,7 +6,7 @@ ...@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2011-2013 Stanford University and the Authors. * * Portions copyright (c) 2011-2014 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -136,9 +136,9 @@ double ReferenceCalcDrudeForceKernel::execute(ContextImpl& context, bool include ...@@ -136,9 +136,9 @@ double ReferenceCalcDrudeForceKernel::execute(ContextImpl& context, bool include
RealOpenMM a1 = (p2 == -1 ? 1 : aniso12[i]); RealOpenMM a1 = (p2 == -1 ? 1 : aniso12[i]);
RealOpenMM a2 = (p3 == -1 || p4 == -1 ? 1 : aniso34[i]); RealOpenMM a2 = (p3 == -1 || p4 == -1 ? 1 : aniso34[i]);
RealOpenMM a3 = 3-a1-a2; RealOpenMM a3 = 3-a1-a2;
RealOpenMM k3 = charge[i]*charge[i]/(polarizability[i]*a3); RealOpenMM k3 = ONE_4PI_EPS0*charge[i]*charge[i]/(polarizability[i]*a3);
RealOpenMM k1 = charge[i]*charge[i]/(polarizability[i]*a1) - k3; RealOpenMM k1 = ONE_4PI_EPS0*charge[i]*charge[i]/(polarizability[i]*a1) - k3;
RealOpenMM k2 = charge[i]*charge[i]/(polarizability[i]*a2) - k3; RealOpenMM k2 = ONE_4PI_EPS0*charge[i]*charge[i]/(polarizability[i]*a2) - k3;
// Compute the isotropic force. // Compute the isotropic force.
...@@ -188,6 +188,7 @@ double ReferenceCalcDrudeForceKernel::execute(ContextImpl& context, bool include ...@@ -188,6 +188,7 @@ double ReferenceCalcDrudeForceKernel::execute(ContextImpl& context, bool include
int dipole2 = pair2[i]; int dipole2 = pair2[i];
int dipole1Particles[] = {particle[dipole1], particle1[dipole1]}; int dipole1Particles[] = {particle[dipole1], particle1[dipole1]};
int dipole2Particles[] = {particle[dipole2], particle1[dipole2]}; int dipole2Particles[] = {particle[dipole2], particle1[dipole2]};
RealOpenMM uscale = pairThole[i]/pow(polarizability[dipole1]*polarizability[dipole2], 1.0/6.0);
for (int j = 0; j < 2; j++) for (int j = 0; j < 2; j++)
for (int k = 0; k < 2; k++) { for (int k = 0; k < 2; k++) {
int p1 = dipole1Particles[j]; int p1 = dipole1Particles[j];
...@@ -195,10 +196,10 @@ double ReferenceCalcDrudeForceKernel::execute(ContextImpl& context, bool include ...@@ -195,10 +196,10 @@ double ReferenceCalcDrudeForceKernel::execute(ContextImpl& context, bool include
RealOpenMM chargeProduct = charge[dipole1]*charge[dipole2]*(j == k ? 1 : -1); RealOpenMM chargeProduct = charge[dipole1]*charge[dipole2]*(j == k ? 1 : -1);
RealVec delta = pos[p1]-pos[p2]; RealVec delta = pos[p1]-pos[p2];
RealOpenMM r = sqrt(delta.dot(delta)); RealOpenMM r = sqrt(delta.dot(delta));
RealOpenMM u = r*pairThole[i]/pow(polarizability[dipole1]*polarizability[dipole2], 1.0/6.0); RealOpenMM u = r*uscale;
RealOpenMM screening = 1.0 - (1.0+0.5*u)*exp(-u); RealOpenMM screening = 1.0 - (1.0+0.5*u)*exp(-u);
energy += ONE_4PI_EPS0*chargeProduct*screening/r; energy += ONE_4PI_EPS0*chargeProduct*screening/r;
RealVec f = delta*(ONE_4PI_EPS0*chargeProduct*screening/(r*r*r)); RealVec f = delta*(ONE_4PI_EPS0*chargeProduct/(r*r))*(screening/r-0.5*(1+u)*exp(-u)*uscale);
force[p1] += f; force[p1] += f;
force[p2] -= f; force[p2] -= f;
} }
...@@ -461,4 +462,4 @@ void ReferenceIntegrateDrudeSCFStepKernel::minimize(ContextImpl& context, double ...@@ -461,4 +462,4 @@ void ReferenceIntegrateDrudeSCFStepKernel::minimize(ContextImpl& context, double
lbfgsfloatval_t fx; lbfgsfloatval_t fx;
MinimizerData data(context, drudeParticles); MinimizerData data(context, drudeParticles);
lbfgs(numDrudeParticles*3, minimizerPos, &fx, evaluate, NULL, &data, &minimizerParams); lbfgs(numDrudeParticles*3, minimizerPos, &fx, evaluate, NULL, &data, &minimizerParams);
} }
\ No newline at end of file
plugins/drude/platforms/reference/tests/TestReferenceDrudeForce.cpp
View file @ 46479322
...@@ -71,14 +71,14 @@ void validateForce(System& system, vector<Vec3>& positions, double expectedEnerg ...@@ -71,14 +71,14 @@ void validateForce(System& system, vector<Vec3>& positions, double expectedEnerg
offsetPos[i][j] = positions[i][j]+offset; offsetPos[i][j] = positions[i][j]+offset;
context.setPositions(offsetPos); context.setPositions(offsetPos);
double e2 = context.getState(State::Energy | State::Forces).getPotentialEnergy(); double e2 = context.getState(State::Energy | State::Forces).getPotentialEnergy();
ASSERT_EQUAL_TOL(state.getForces()[i][j], (e1-e2)/(2*offset), 1e-3); ASSERT_EQUAL_TOL(state.getForces()[i][j], (e1-e2)/(2*offset), 1e-5);
} }
} }
void testSingleParticle() { void testSingleParticle() {
const double k = 1.5; const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1; const double charge = 0.1;
const double alpha = charge*charge/k; const double alpha = ONE_4PI_EPS0*charge*charge/k;
System system; System system;
system.addParticle(1.0); system.addParticle(1.0);
system.addParticle(1.0); system.addParticle(1.0);
...@@ -92,9 +92,9 @@ void testSingleParticle() { ...@@ -92,9 +92,9 @@ void testSingleParticle() {
} }
void testAnisotropicParticle() { void testAnisotropicParticle() {
const double k = 1.5; const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1; const double charge = 0.1;
const double alpha = charge*charge/k; const double alpha = ONE_4PI_EPS0*charge*charge/k;
const double a1 = 0.8; const double a1 = 0.8;
const double a2 = 1.1; const double a2 = 1.1;
const double k1 = k/a1; const double k1 = k/a1;
...@@ -124,9 +124,9 @@ double computeScreening(double r, double thole, double alpha1, double alpha2) { ...@@ -124,9 +124,9 @@ double computeScreening(double r, double thole, double alpha1, double alpha2) {
} }
void testThole() { void testThole() {
const double k = 1.5; const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1; const double charge = 0.1;
const double alpha = charge*charge/k; const double alpha = ONE_4PI_EPS0*charge*charge/k;
const double thole = 2.5; const double thole = 2.5;
System system; System system;
system.addParticle(1.0); system.addParticle(1.0);
...@@ -157,9 +157,9 @@ void testThole() { ...@@ -157,9 +157,9 @@ void testThole() {
} }
void testChangingParameters() { void testChangingParameters() {
const double k = 1.5; const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1; const double charge = 0.1;
const double alpha = charge*charge/k; const double alpha = ONE_4PI_EPS0*charge*charge/k;
Platform& platform = Platform::getPlatformByName("Reference"); Platform& platform = Platform::getPlatformByName("Reference");
// Create the system. // Create the system.
...@@ -184,9 +184,9 @@ void testChangingParameters() { ...@@ -184,9 +184,9 @@ void testChangingParameters() {
// Modify the parameters. // Modify the parameters.
const double k2 = 2.2; const double k2 = ONE_4PI_EPS0*2.2;
const double charge2 = 0.3; const double charge2 = 0.3;
const double alpha2 = charge2*charge2/k2; const double alpha2 = ONE_4PI_EPS0*charge2*charge2/k2;
drude->setParticleParameters(0, 1, 0, -1, -1, -1, charge2, alpha2, 1, 1); drude->setParticleParameters(0, 1, 0, -1, -1, -1, charge2, alpha2, 1, 1);
drude->updateParametersInContext(context); drude->updateParametersInContext(context);
state = context.getState(State::Energy); state = context.getState(State::Energy);
......
plugins/drude/platforms/reference/tests/TestReferenceDrudeLangevinIntegrator.cpp
View file @ 46479322
...@@ -53,9 +53,9 @@ extern "C" OPENMM_EXPORT void registerDrudeReferenceKernelFactories(); ...@@ -53,9 +53,9 @@ extern "C" OPENMM_EXPORT void registerDrudeReferenceKernelFactories();
void testSinglePair() { void testSinglePair() {
const double temperature = 300.0; const double temperature = 300.0;
const double temperatureDrude = 10.0; const double temperatureDrude = 10.0;
const double k = 1.5; const double k = ONE_4PI_EPS0*1.5;
const double charge = 0.1; const double charge = 0.1;
const double alpha = charge*charge/k; const double alpha = ONE_4PI_EPS0*charge*charge/k;
const double mass1 = 1.0; const double mass1 = 1.0;
const double mass2 = 0.1; const double mass2 = 0.1;
const double totalMass = mass1+mass2; const double totalMass = mass1+mass2;
...@@ -132,7 +132,7 @@ void testWater() { ...@@ -132,7 +132,7 @@ void testWater() {
system.addConstraint(startIndex, startIndex+3, 0.09572); system.addConstraint(startIndex, startIndex+3, 0.09572);
system.addConstraint(startIndex+2, startIndex+3, 0.15139); system.addConstraint(startIndex+2, startIndex+3, 0.15139);
system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721)); system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721));
drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, 1.71636*1.71636/(100000*4.184), 1, 1); drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, ONE_4PI_EPS0*1.71636*1.71636/(100000*4.184), 1, 1);
} }
vector<Vec3> positions; vector<Vec3> positions;
for (int i = 0; i < gridSize; i++) for (int i = 0; i < gridSize; i++)
......
plugins/drude/platforms/reference/tests/TestReferenceDrudeSCFIntegrator.cpp
View file @ 46479322
...@@ -85,7 +85,7 @@ void testWater() { ...@@ -85,7 +85,7 @@ void testWater() {
system.addConstraint(startIndex, startIndex+3, 0.09572); system.addConstraint(startIndex, startIndex+3, 0.09572);
system.addConstraint(startIndex+2, startIndex+3, 0.15139); system.addConstraint(startIndex+2, startIndex+3, 0.15139);
system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721)); system.setVirtualSite(startIndex+4, new ThreeParticleAverageSite(startIndex, startIndex+2, startIndex+3, 0.786646558, 0.106676721, 0.106676721));
drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, 1.71636*1.71636/(100000*4.184), 1, 1); drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.71636, ONE_4PI_EPS0*1.71636*1.71636/(100000*4.184), 1, 1);
} }
vector<Vec3> positions; vector<Vec3> positions;
for (int i = 0; i < gridSize; i++) for (int i = 0; i < gridSize; i++)
......
wrappers/python/simtk/openmm/app/data/charmm_polar_2013.xml 0 → 100644
View file @ 46479322
This source diff could not be displayed because it is too large. You can view the blob instead.
wrappers/python/simtk/openmm/app/data/swm4ndp.xml
View file @ 46479322
...@@ -30,7 +30,7 @@ ...@@ -30,7 +30,7 @@
<Atom type="swm4ndp-OD" charge="-1.71636" sigma="1" epsilon="0"/> <Atom type="swm4ndp-OD" charge="-1.71636" sigma="1" epsilon="0"/>
</NonbondedForce> </NonbondedForce>
<DrudeForce> <DrudeForce>
<Particle type1="swm4ndp-OD" type2="swm4ndp-O" charge="-1.71636" polarizability="7.040850e-6" thole="1.3"/> <Particle type1="swm4ndp-OD" type2="swm4ndp-O" charge="-1.71636" polarizability="0.000978253" thole="1.3"/>
</DrudeForce> </DrudeForce>
</ForceField> </ForceField>
wrappers/python/simtk/openmm/app/forcefield.py
View file @ 46479322
...@@ -240,6 +240,7 @@ class ForceField(object): ...@@ -240,6 +240,7 @@ class ForceField(object):
def __init__(self): def __init__(self):
self.atomType = {} self.atomType = {}
self.atoms = [] self.atoms = []
self.excludeAtomWith = []
self.virtualSites = {} self.virtualSites = {}
self.bonds = [] self.bonds = []
self.angles = [] self.angles = []
...@@ -302,6 +303,10 @@ class ForceField(object): ...@@ -302,6 +303,10 @@ class ForceField(object):
self.localPos = [float(attrib['p1']), float(attrib['p2']), float(attrib['p3'])] self.localPos = [float(attrib['p1']), float(attrib['p2']), float(attrib['p3'])]
else: else:
raise ValueError('Unknown virtual site type: %s' % self.type) raise ValueError('Unknown virtual site type: %s' % self.type)
if 'excludeWith' in attrib:
self.excludeWith = int(attrib['excludeWith'])
else:
self.excludeWith = self.atoms[0]
def createSystem(self, topology, nonbondedMethod=NoCutoff, nonbondedCutoff=1.0*unit.nanometer, def createSystem(self, topology, nonbondedMethod=NoCutoff, nonbondedCutoff=1.0*unit.nanometer,
constraints=None, rigidWater=True, removeCMMotion=True, hydrogenMass=None, **args): constraints=None, rigidWater=True, removeCMMotion=True, hydrogenMass=None, **args):
...@@ -324,6 +329,8 @@ class ForceField(object): ...@@ -324,6 +329,8 @@ class ForceField(object):
""" """
data = ForceField._SystemData() data = ForceField._SystemData()
data.atoms = list(topology.atoms()) data.atoms = list(topology.atoms())
for atom in data.atoms:
data.excludeAtomWith.append([])
# Make a list of all bonds # Make a list of all bonds
...@@ -363,7 +370,7 @@ class ForceField(object): ...@@ -363,7 +370,7 @@ class ForceField(object):
data.atomType[atom] = template.atoms[match].type data.atomType[atom] = template.atoms[match].type
for site in template.virtualSites: for site in template.virtualSites:
if match == site.index: if match == site.index:
data.virtualSites[atom] = (site, [matchAtoms[i].index for i in site.atoms]) data.virtualSites[atom] = (site, [matchAtoms[i].index for i in site.atoms], matchAtoms[site.excludeWith].index)
# Create the System and add atoms # Create the System and add atoms
...@@ -478,8 +485,9 @@ class ForceField(object): ...@@ -478,8 +485,9 @@ class ForceField(object):
# Add virtual sites # Add virtual sites
for atom in data.virtualSites: for atom in data.virtualSites:
(site, atoms) = data.virtualSites[atom] (site, atoms, excludeWith) = data.virtualSites[atom]
index = atom.index index = atom.index
data.excludeAtomWith[excludeWith].append(index)
if site.type == 'average2': if site.type == 'average2':
sys.setVirtualSite(index, mm.TwoParticleAverageSite(atoms[0], atoms[1], site.weights[0], site.weights[1])) sys.setVirtualSite(index, mm.TwoParticleAverageSite(atoms[0], atoms[1], site.weights[0], site.weights[1]))
elif site.type == 'average3': elif site.type == 'average3':
...@@ -895,7 +903,7 @@ class PeriodicTorsionGenerator: ...@@ -895,7 +903,7 @@ class PeriodicTorsionGenerator:
for (t2, t3, t4) in itertools.permutations(((type2, 1), (type3, 2), (type4, 3))): for (t2, t3, t4) in itertools.permutations(((type2, 1), (type3, 2), (type4, 3))):
if t2[0] in types2 and t3[0] in types3 and t4[0] in types4: if t2[0] in types2 and t3[0] in types3 and t4[0] in types4:
# Workaround to be more consistent with AMBER. It uses wildcards to define most of its # Workaround to be more consistent with AMBER. It uses wildcards to define most of its
# impropers, which leaves the ordering ambigous. It then follows some bizarre rules # impropers, which leaves the ordering ambiguous. It then follows some bizarre rules
# to pick the order. # to pick the order.
a1 = torsion[t2[1]] a1 = torsion[t2[1]]
a2 = torsion[t3[1]] a2 = torsion[t3[1]]
...@@ -991,18 +999,22 @@ class RBTorsionGenerator: ...@@ -991,18 +999,22 @@ class RBTorsionGenerator:
if type1 in types1: if type1 in types1:
for (t2, t3, t4) in itertools.permutations(((type2, 1), (type3, 2), (type4, 3))): for (t2, t3, t4) in itertools.permutations(((type2, 1), (type3, 2), (type4, 3))):
if t2[0] in types2 and t3[0] in types3 and t4[0] in types4: if t2[0] in types2 and t3[0] in types3 and t4[0] in types4:
# Workaround to be more consistent with AMBER. It uses wildcards to define most of its if wildcard in (types1, types2, types3, types4):
# impropers, which leaves the ordering ambigous. It then follows some bizarre rules # Workaround to be more consistent with AMBER. It uses wildcards to define most of its
# to pick the order. # impropers, which leaves the ordering ambiguous. It then follows some bizarre rules
a1 = torsion[t2[1]] # to pick the order.
a2 = torsion[t3[1]] a1 = torsion[t2[1]]
e1 = data.atoms[a1].element a2 = torsion[t3[1]]
e2 = data.atoms[a2].element e1 = data.atoms[a1].element
if e1 == e2 and a1 > a2: e2 = data.atoms[a2].element
(a1, a2) = (a2, a1) if e1 == e2 and a1 > a2:
elif e1 != elem.carbon and (e2 == elem.carbon or e1.mass < e2.mass): (a1, a2) = (a2, a1)
(a1, a2) = (a2, a1) elif e1 != elem.carbon and (e2 == elem.carbon or e1.mass < e2.mass):
force.addTorsion(a1, a2, torsion[0], torsion[t4[1]], tordef.c[0], tordef.c[1], tordef.c[2], tordef.c[3], tordef.c[4], tordef.c[5]) (a1, a2) = (a2, a1)
force.addTorsion(a1, a2, torsion[0], torsion[t4[1]], tordef.c[0], tordef.c[1], tordef.c[2], tordef.c[3], tordef.c[4], tordef.c[5])
else:
# There are no wildcards, so the order is unambiguous.
force.addTorsion(torsion[0], torsion[t2[1]], torsion[t3[1]], torsion[t4[1]], tordef.c[0], tordef.c[1], tordef.c[2], tordef.c[3], tordef.c[4], tordef.c[5])
done = True done = True
break break
...@@ -1157,33 +1169,33 @@ class NonbondedGenerator: ...@@ -1157,33 +1169,33 @@ class NonbondedGenerator:
sys.addForce(force) sys.addForce(force)
def postprocessSystem(self, sys, data, args): def postprocessSystem(self, sys, data, args):
# Create exceptions based on bonds, virtual sites, and Drude particles. # Create exceptions based on bonds.
bondIndices = [] bondIndices = []
for bond in data.bonds: for bond in data.bonds:
bondIndices.append((bond.atom1, bond.atom2)) bondIndices.append((bond.atom1, bond.atom2))
# If a virtual site does *not* share exclusions with another atom, add a bond between it and its first parent atom.
for i in range(sys.getNumParticles()): for i in range(sys.getNumParticles()):
if sys.isVirtualSite(i): if sys.isVirtualSite(i):
site = sys.getVirtualSite(i) (site, atoms, excludeWith) = data.virtualSites[data.atoms[i]]
for j in range(site.getNumParticles()): if excludeWith is None:
bondIndices.append((i, site.getParticle(j))) bondIndices.append((i, site.getParticle(0)))
drude = [f for f in sys.getForces() if isinstance(f, mm.DrudeForce)]
if len(drude) > 0: # Certain particles, such as lone pairs and Drude particles, share exclusions with a parent atom.
drude = drude[0] # If the parent atom does not interact with an atom, the child particle does not either.
# For purposes of creating exceptions, a Drude particle is "bonded" to anything
# its parent atom is bonded to. for atom1, atom2 in bondIndices:
drudeMap = {} for child1 in data.excludeAtomWith[atom1]:
for i in range(drude.getNumParticles()): bondIndices.append((child1, atom2))
params = drude.getParticleParameters(i) for child2 in data.excludeAtomWith[atom2]:
drudeMap[params[1]] = params[0] bondIndices.append((child1, child2))
for atom1, atom2 in bondIndices: for child2 in data.excludeAtomWith[atom2]:
drude1 = drudeMap[atom1] if atom1 in drudeMap else None bondIndices.append((atom1, child2))
drude2 = drudeMap[atom2] if atom2 in drudeMap else None
if drude1 is not None: # Create the exceptions.
bondIndices.append((drude1, atom2))
if drude2 is not None:
bondIndices.append((drude1, drude2))
if drude2 is not None:
bondIndices.append((atom1, drude2))
nonbonded = [f for f in sys.getForces() if isinstance(f, mm.NonbondedForce)][0] nonbonded = [f for f in sys.getForces() if isinstance(f, mm.NonbondedForce)][0]
nonbonded.createExceptionsFromBonds(bondIndices, self.coulomb14scale, self.lj14scale) nonbonded.createExceptionsFromBonds(bondIndices, self.coulomb14scale, self.lj14scale)
...@@ -1519,18 +1531,22 @@ class CustomTorsionGenerator: ...@@ -1519,18 +1531,22 @@ class CustomTorsionGenerator:
if type1 in types1: if type1 in types1:
for (t2, t3, t4) in itertools.permutations(((type2, 1), (type3, 2), (type4, 3))): for (t2, t3, t4) in itertools.permutations(((type2, 1), (type3, 2), (type4, 3))):
if t2[0] in types2 and t3[0] in types3 and t4[0] in types4: if t2[0] in types2 and t3[0] in types3 and t4[0] in types4:
# Workaround to be more consistent with AMBER. It uses wildcards to define most of its if wildcard in (types1, types2, types3, types4):
# impropers, which leaves the ordering ambigous. It then follows some bizarre rules # Workaround to be more consistent with AMBER. It uses wildcards to define most of its
# to pick the order. # impropers, which leaves the ordering ambiguous. It then follows some bizarre rules
a1 = torsion[t2[1]] # to pick the order.
a2 = torsion[t3[1]] a1 = torsion[t2[1]]
e1 = data.atoms[a1].element a2 = torsion[t3[1]]
e2 = data.atoms[a2].element e1 = data.atoms[a1].element
if e1 == e2 and a1 > a2: e2 = data.atoms[a2].element
(a1, a2) = (a2, a1) if e1 == e2 and a1 > a2:
elif e1 != elem.carbon and (e2 == elem.carbon or e1.mass < e2.mass): (a1, a2) = (a2, a1)
(a1, a2) = (a2, a1) elif e1 != elem.carbon and (e2 == elem.carbon or e1.mass < e2.mass):
force.addTorsion(a1, a2, torsion[0], torsion[t4[1]], tordef.paramValues) (a1, a2) = (a2, a1)
force.addTorsion(a1, a2, torsion[0], torsion[t4[1]], tordef.paramValues)
else:
# There are no wildcards, so the order is unambiguous.
force.addTorsion(torsion[0], torsion[t2[1]], torsion[t3[1]], torsion[t4[1]], tordef.paramValues)
done = True done = True
break break
...@@ -4290,8 +4306,6 @@ class DrudeGenerator: ...@@ -4290,8 +4306,6 @@ class DrudeGenerator:
# Add Drude particles. # Add Drude particles.
drudeMap = {}
parentMap = {}
for atom in data.atoms: for atom in data.atoms:
t = data.atomType[atom] t = data.atomType[atom]
if t in self.typeMap: if t in self.typeMap:
...@@ -4308,9 +4322,8 @@ class DrudeGenerator: ...@@ -4308,9 +4322,8 @@ class DrudeGenerator:
p[2] = atom2.index p[2] = atom2.index
elif values[3] is not None and type2 in values[3]: elif values[3] is not None and type2 in values[3]:
p[3] = atom2.index p[3] = atom2.index
drudeIndex = force.addParticle(atom.index, p[0], p[1], p[2], p[3], values[4], values[5], values[6], values[7]) force.addParticle(atom.index, p[0], p[1], p[2], p[3], values[4], values[5], values[6], values[7])
drudeMap[atom.index] = p[0] data.excludeAtomWith[p[0]].append(atom.index)
parentMap[p[0]] = (atom.index, drudeIndex)
sys.addForce(force) sys.addForce(force)
def postprocessSystem(self, sys, data, args): def postprocessSystem(self, sys, data, args):
...@@ -4323,14 +4336,14 @@ class DrudeGenerator: ...@@ -4323,14 +4336,14 @@ class DrudeGenerator:
particleMap[drude.getParticleParameters(i)[0]] = i particleMap[drude.getParticleParameters(i)[0]] = i
for i in range(nonbonded.getNumExceptions()): for i in range(nonbonded.getNumExceptions()):
(particle1, particle2, charge, sigma, epsilon) = nonbonded.getExceptionParameters(i) (particle1, particle2, charge, sigma, epsilon) = nonbonded.getExceptionParameters(i)
if charge == 0 and epsilon == 0: if charge._value == 0 and epsilon._value == 0:
# This is an exclusion. # This is an exclusion.
if particle1 in particleMap and particle2 in particleMap: if particle1 in particleMap and particle2 in particleMap:
# It connects two Drude particles, so add a screened pair. # It connects two Drude particles, so add a screened pair.
drude1 = particleMap[particle1] drude1 = particleMap[particle1]
drude2 = particleMap[particle2] drude2 = particleMap[particle2]
type1 = data.atomType[data.atoms[drude1]] type1 = data.atomType[data.atoms[particle1]]
type2 = data.atomType[data.atoms[drude2]] type2 = data.atomType[data.atoms[particle2]]
thole1 = self.typeMap[type1][8] thole1 = self.typeMap[type1][8]
thole2 = self.typeMap[type2][8] thole2 = self.typeMap[type2][8]
drude.addScreenedPair(drude1, drude2, thole1+thole2) drude.addScreenedPair(drude1, drude2, thole1+thole2)
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment