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tsoc
openmm
Commits
167ae8a0
Commit
167ae8a0
authored
Nov 19, 2015
by
peastman
Browse files
Merge pull request #1271 from peastman/gbvi
Deleted GBVIForce
parents
b20c20fe
14e78600
Changes
32
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12 changed files
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1 addition
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8311 deletions
+1
-8311
platforms/reference/tests/TestReferenceGBVIForce.cpp
platforms/reference/tests/TestReferenceGBVIForce.cpp
+0
-247
serialization/include/openmm/serialization/GBVIForceProxy.h
serialization/include/openmm/serialization/GBVIForceProxy.h
+0
-53
serialization/src/GBVIForceProxy.cpp
serialization/src/GBVIForceProxy.cpp
+0
-103
serialization/src/SerializationProxyRegistration.cpp
serialization/src/SerializationProxyRegistration.cpp
+0
-3
serialization/tests/TestSerializeGBVIForce.cpp
serialization/tests/TestSerializeGBVIForce.cpp
+0
-108
wrappers/python/simtk/openmm/app/data/amber03_gbvi.xml
wrappers/python/simtk/openmm/app/data/amber03_gbvi.xml
+0
-1954
wrappers/python/simtk/openmm/app/data/amber10_gbvi.xml
wrappers/python/simtk/openmm/app/data/amber10_gbvi.xml
+0
-1829
wrappers/python/simtk/openmm/app/data/amber96_gbvi.xml
wrappers/python/simtk/openmm/app/data/amber96_gbvi.xml
+0
-1958
wrappers/python/simtk/openmm/app/data/amber99_gbvi.xml
wrappers/python/simtk/openmm/app/data/amber99_gbvi.xml
+0
-1958
wrappers/python/simtk/openmm/app/forcefield.py
wrappers/python/simtk/openmm/app/forcefield.py
+0
-86
wrappers/python/simtk/openmm/app/internal/amber_file_parser.py
...ers/python/simtk/openmm/app/internal/amber_file_parser.py
+1
-3
wrappers/python/src/swig_doxygen/swigInputConfig.py
wrappers/python/src/swig_doxygen/swigInputConfig.py
+0
-9
No files found.
platforms/reference/tests/TestReferenceGBVIForce.cpp
deleted
100644 → 0
View file @
b20c20fe
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the reference implementation of GBVIForce.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "ReferencePlatform.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/GBVIForce.h"
#include "openmm/GBSAOBCForce.h"
#include "openmm/System.h"
#include "openmm/LangevinIntegrator.h"
#include "openmm/NonbondedForce.h"
#include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using
namespace
OpenMM
;
using
namespace
std
;
ReferencePlatform
platform
;
const
double
TOL
=
1e-5
;
void
testSingleParticle
()
{
System
system
;
system
.
addParticle
(
2.0
);
LangevinIntegrator
integrator
(
0
,
0.1
,
0.01
);
GBVIForce
*
forceField
=
new
GBVIForce
();
double
charge
=
-
1.0
;
double
radius
=
0.15
;
double
gamma
=
1.0
;
forceField
->
addParticle
(
charge
,
radius
,
gamma
);
system
.
addForce
(
forceField
);
ASSERT
(
!
forceField
->
usesPeriodicBoundaryConditions
());
ASSERT
(
!
system
.
usesPeriodicBoundaryConditions
());
Context
context
(
system
,
integrator
,
platform
);
vector
<
Vec3
>
positions
(
1
);
positions
[
0
]
=
Vec3
(
0
,
0
,
0
);
context
.
setPositions
(
positions
);
State
state
=
context
.
getState
(
State
::
Energy
);
double
bornRadius
=
radius
;
double
eps0
=
EPSILON0
;
double
tau
=
(
1.0
/
forceField
->
getSoluteDielectric
()
-
1.0
/
forceField
->
getSolventDielectric
());
double
bornEnergy
=
(
-
charge
*
charge
/
(
8
*
PI_M
*
eps0
))
*
tau
/
bornRadius
;
double
nonpolarEnergy
=
-
gamma
*
tau
*
std
::
pow
(
radius
/
bornRadius
,
3.0
);
double
expectedE
=
(
bornEnergy
+
nonpolarEnergy
);
double
obtainedE
=
state
.
getPotentialEnergy
();
double
diff
=
fabs
((
obtainedE
-
expectedE
)
/
expectedE
);
ASSERT_EQUAL_TOL
((
bornEnergy
+
nonpolarEnergy
),
state
.
getPotentialEnergy
(),
0.01
);
}
void
testEnergyEthane
(
int
applyBornRadiiScaling
)
{
const
int
numParticles
=
8
;
System
system
;
LangevinIntegrator
integrator
(
0
,
0.1
,
0.01
);
// harmonic bond
double
C_HBondDistance
=
0.1097
;
double
C_CBondDistance
=
0.1504
;
HarmonicBondForce
*
bonds
=
new
HarmonicBondForce
();
bonds
->
addBond
(
0
,
1
,
C_HBondDistance
,
0.0
);
bonds
->
addBond
(
2
,
1
,
C_HBondDistance
,
0.0
);
bonds
->
addBond
(
3
,
1
,
C_HBondDistance
,
0.0
);
bonds
->
addBond
(
1
,
4
,
C_CBondDistance
,
0.0
);
bonds
->
addBond
(
5
,
4
,
C_HBondDistance
,
0.0
);
bonds
->
addBond
(
6
,
4
,
C_HBondDistance
,
0.0
);
bonds
->
addBond
(
7
,
4
,
C_HBondDistance
,
0.0
);
system
.
addForce
(
bonds
);
double
C_radius
,
C_gamma
,
C_charge
,
H_radius
,
H_gamma
,
H_charge
;
int
AM1_BCC
=
1
;
H_charge
=
-
0.053
;
C_charge
=
-
3.0
*
H_charge
;
if
(
AM1_BCC
)
{
C_radius
=
0.180
;
C_gamma
=
-
0.2863
;
H_radius
=
0.125
;
H_gamma
=
0.2437
;
}
else
{
C_radius
=
0.215
;
C_gamma
=
-
1.1087
;
H_radius
=
0.150
;
H_gamma
=
0.1237
;
}
NonbondedForce
*
nonbonded
=
new
NonbondedForce
();
nonbonded
->
setNonbondedMethod
(
NonbondedForce
::
NoCutoff
);
GBVIForce
*
forceField
=
new
GBVIForce
();
if
(
applyBornRadiiScaling
)
{
forceField
->
setBornRadiusScalingMethod
(
GBVIForce
::
QuinticSpline
);
}
else
{
forceField
->
setBornRadiusScalingMethod
(
GBVIForce
::
NoScaling
);
}
for
(
int
i
=
0
;
i
<
numParticles
;
i
++
)
{
system
.
addParticle
(
1.0
);
forceField
->
addParticle
(
H_charge
,
H_radius
,
H_gamma
);
nonbonded
->
addParticle
(
H_charge
,
H_radius
,
0.0
);
}
forceField
->
setParticleParameters
(
1
,
C_charge
,
C_radius
,
C_gamma
);
forceField
->
setParticleParameters
(
4
,
C_charge
,
C_radius
,
C_gamma
);
nonbonded
->
setParticleParameters
(
1
,
C_charge
,
C_radius
,
0.0
);
nonbonded
->
setParticleParameters
(
4
,
C_charge
,
C_radius
,
0.0
);
forceField
->
addBond
(
0
,
1
,
C_HBondDistance
);
forceField
->
addBond
(
2
,
1
,
C_HBondDistance
);
forceField
->
addBond
(
3
,
1
,
C_HBondDistance
);
forceField
->
addBond
(
1
,
4
,
C_CBondDistance
);
forceField
->
addBond
(
5
,
4
,
C_HBondDistance
);
forceField
->
addBond
(
6
,
4
,
C_HBondDistance
);
forceField
->
addBond
(
7
,
4
,
C_HBondDistance
);
std
::
vector
<
pair
<
int
,
int
>
>
bondExceptions
;
std
::
vector
<
double
>
bondDistances
;
bondExceptions
.
push_back
(
pair
<
int
,
int
>
(
0
,
1
));
bondDistances
.
push_back
(
C_HBondDistance
);
bondExceptions
.
push_back
(
pair
<
int
,
int
>
(
2
,
1
));
bondDistances
.
push_back
(
C_HBondDistance
);
bondExceptions
.
push_back
(
pair
<
int
,
int
>
(
3
,
1
));
bondDistances
.
push_back
(
C_HBondDistance
);
bondExceptions
.
push_back
(
pair
<
int
,
int
>
(
1
,
4
));
bondDistances
.
push_back
(
C_CBondDistance
);
bondExceptions
.
push_back
(
pair
<
int
,
int
>
(
5
,
4
));
bondDistances
.
push_back
(
C_HBondDistance
);
bondExceptions
.
push_back
(
pair
<
int
,
int
>
(
6
,
4
));
bondDistances
.
push_back
(
C_HBondDistance
);
bondExceptions
.
push_back
(
pair
<
int
,
int
>
(
7
,
4
));
bondDistances
.
push_back
(
C_HBondDistance
);
nonbonded
->
createExceptionsFromBonds
(
bondExceptions
,
0.0
,
0.0
);
system
.
addForce
(
forceField
);
system
.
addForce
(
nonbonded
);
Context
context
(
system
,
integrator
,
platform
);
vector
<
Vec3
>
positions
(
numParticles
);
positions
[
0
]
=
Vec3
(
0.5480
,
1.7661
,
0.0000
);
positions
[
1
]
=
Vec3
(
0.7286
,
0.8978
,
0.6468
);
positions
[
2
]
=
Vec3
(
0.4974
,
0.0000
,
0.0588
);
positions
[
3
]
=
Vec3
(
0.0000
,
0.9459
,
1.4666
);
positions
[
4
]
=
Vec3
(
2.1421
,
0.8746
,
1.1615
);
positions
[
5
]
=
Vec3
(
2.3239
,
0.0050
,
1.8065
);
positions
[
6
]
=
Vec3
(
2.8705
,
0.8295
,
0.3416
);
positions
[
7
]
=
Vec3
(
2.3722
,
1.7711
,
1.7518
);
context
.
setPositions
(
positions
);
State
state
=
context
.
getState
(
State
::
Forces
|
State
::
Energy
);
// Take a small step in the direction of the energy gradient.
double
norm
=
0.0
;
double
forceSum
[
3
]
=
{
0.0
,
0.0
,
0.0
};
for
(
int
i
=
0
;
i
<
numParticles
;
++
i
)
{
Vec3
f
=
state
.
getForces
()[
i
];
norm
+=
f
[
0
]
*
f
[
0
]
+
f
[
1
]
*
f
[
1
]
+
f
[
2
]
*
f
[
2
];
forceSum
[
0
]
+=
f
[
0
];
forceSum
[
1
]
+=
f
[
1
];
forceSum
[
2
]
+=
f
[
2
];
}
norm
=
std
::
sqrt
(
norm
);
const
double
delta
=
1e-4
;
double
step
=
delta
/
norm
;
for
(
int
i
=
0
;
i
<
numParticles
;
++
i
)
{
Vec3
p
=
positions
[
i
];
Vec3
f
=
state
.
getForces
()[
i
];
positions
[
i
]
=
Vec3
(
p
[
0
]
-
f
[
0
]
*
step
,
p
[
1
]
-
f
[
1
]
*
step
,
p
[
2
]
-
f
[
2
]
*
step
);
}
context
.
setPositions
(
positions
);
State
state2
=
context
.
getState
(
State
::
Energy
);
// See whether the potential energy changed by the expected amount.
ASSERT_EQUAL_TOL
(
norm
,
(
state2
.
getPotentialEnergy
()
-
state
.
getPotentialEnergy
())
/
delta
,
0.01
)
}
int
main
()
{
try
{
testSingleParticle
();
testEnergyEthane
(
0
);
testEnergyEthane
(
1
);
}
catch
(
const
exception
&
e
)
{
cout
<<
"exception: "
<<
e
.
what
()
<<
endl
;
return
1
;
}
cout
<<
"Done"
<<
endl
;
return
0
;
}
serialization/include/openmm/serialization/GBVIForceProxy.h
deleted
100644 → 0
View file @
b20c20fe
#ifndef OPENMM_GBVIFORCE_PROXY_H_
#define OPENMM_GBVIFORCE_PROXY_H_
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/internal/windowsExport.h"
#include "openmm/serialization/SerializationProxy.h"
namespace
OpenMM
{
/**
* This is a proxy for serializing GBVIForce objects.
*/
class
OPENMM_EXPORT
GBVIForceProxy
:
public
SerializationProxy
{
public:
GBVIForceProxy
();
void
serialize
(
const
void
*
object
,
SerializationNode
&
node
)
const
;
void
*
deserialize
(
const
SerializationNode
&
node
)
const
;
};
}
// namespace OpenMM
#endif
/*OPENMM_GBVIFORCE_PROXY_H_*/
serialization/src/GBVIForceProxy.cpp
deleted
100644 → 0
View file @
b20c20fe
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/serialization/GBVIForceProxy.h"
#include "openmm/serialization/SerializationNode.h"
#include "openmm/Force.h"
#include "openmm/GBVIForce.h"
#include <sstream>
using
namespace
OpenMM
;
using
namespace
std
;
GBVIForceProxy
::
GBVIForceProxy
()
:
SerializationProxy
(
"GBVIForce"
)
{
}
void
GBVIForceProxy
::
serialize
(
const
void
*
object
,
SerializationNode
&
node
)
const
{
node
.
setIntProperty
(
"version"
,
2
);
const
GBVIForce
&
force
=
*
reinterpret_cast
<
const
GBVIForce
*>
(
object
);
node
.
setIntProperty
(
"forceGroup"
,
force
.
getForceGroup
());
node
.
setIntProperty
(
"method"
,
(
int
)
force
.
getNonbondedMethod
());
node
.
setIntProperty
(
"scalingMethod"
,
(
int
)
force
.
getBornRadiusScalingMethod
());
node
.
setDoubleProperty
(
"quinticLowerLimitFactor"
,
force
.
getQuinticLowerLimitFactor
());
node
.
setDoubleProperty
(
"quinticUpperBornRadiusLimit"
,
force
.
getQuinticUpperBornRadiusLimit
());
node
.
setDoubleProperty
(
"cutoff"
,
force
.
getCutoffDistance
());
node
.
setDoubleProperty
(
"soluteDielectric"
,
force
.
getSoluteDielectric
());
node
.
setDoubleProperty
(
"solventDielectric"
,
force
.
getSolventDielectric
());
SerializationNode
&
particles
=
node
.
createChildNode
(
"Particles"
);
for
(
int
i
=
0
;
i
<
force
.
getNumParticles
();
i
++
)
{
double
charge
,
radius
,
gamma
;
force
.
getParticleParameters
(
i
,
charge
,
radius
,
gamma
);
particles
.
createChildNode
(
"Particle"
).
setDoubleProperty
(
"q"
,
charge
).
setDoubleProperty
(
"r"
,
radius
).
setDoubleProperty
(
"gamma"
,
gamma
);
}
SerializationNode
&
bonds
=
node
.
createChildNode
(
"Bonds"
);
for
(
int
i
=
0
;
i
<
force
.
getNumBonds
();
i
++
)
{
int
particle1
,
particle2
;
double
distance
;
force
.
getBondParameters
(
i
,
particle1
,
particle2
,
distance
);
bonds
.
createChildNode
(
"Bond"
).
setIntProperty
(
"p1"
,
particle1
).
setIntProperty
(
"p2"
,
particle2
).
setDoubleProperty
(
"d"
,
distance
);
}
}
void
*
GBVIForceProxy
::
deserialize
(
const
SerializationNode
&
node
)
const
{
if
(
node
.
getIntProperty
(
"version"
)
!=
1
&&
node
.
getIntProperty
(
"version"
)
!=
2
)
throw
OpenMMException
(
"Unsupported version number"
);
GBVIForce
*
force
=
new
GBVIForce
();
try
{
force
->
setForceGroup
(
node
.
getIntProperty
(
"forceGroup"
,
0
));
force
->
setNonbondedMethod
((
GBVIForce
::
NonbondedMethod
)
node
.
getIntProperty
(
"method"
));
force
->
setCutoffDistance
(
node
.
getDoubleProperty
(
"cutoff"
));
force
->
setSoluteDielectric
(
node
.
getDoubleProperty
(
"soluteDielectric"
));
force
->
setSolventDielectric
(
node
.
getDoubleProperty
(
"solventDielectric"
));
if
(
node
.
getIntProperty
(
"version"
)
>=
2
){
force
->
setBornRadiusScalingMethod
(
(
GBVIForce
::
BornRadiusScalingMethod
)
node
.
getIntProperty
(
"scalingMethod"
));
force
->
setQuinticLowerLimitFactor
(
node
.
getDoubleProperty
(
"quinticLowerLimitFactor"
));
force
->
setQuinticUpperBornRadiusLimit
(
node
.
getDoubleProperty
(
"quinticUpperBornRadiusLimit"
));
}
const
SerializationNode
&
particles
=
node
.
getChildNode
(
"Particles"
);
for
(
int
i
=
0
;
i
<
(
int
)
particles
.
getChildren
().
size
();
i
++
)
{
const
SerializationNode
&
particle
=
particles
.
getChildren
()[
i
];
force
->
addParticle
(
particle
.
getDoubleProperty
(
"q"
),
particle
.
getDoubleProperty
(
"r"
),
particle
.
getDoubleProperty
(
"gamma"
));
}
const
SerializationNode
&
bonds
=
node
.
getChildNode
(
"Bonds"
);
for
(
int
i
=
0
;
i
<
(
int
)
bonds
.
getChildren
().
size
();
i
++
)
{
const
SerializationNode
&
bond
=
bonds
.
getChildren
()[
i
];
force
->
addBond
(
bond
.
getIntProperty
(
"p1"
),
bond
.
getIntProperty
(
"p2"
),
bond
.
getDoubleProperty
(
"d"
));
}
}
catch
(...)
{
delete
force
;
throw
;
}
return
force
;
}
serialization/src/SerializationProxyRegistration.cpp
View file @
167ae8a0
...
...
@@ -45,7 +45,6 @@
#include "openmm/CustomNonbondedForce.h"
#include "openmm/CustomTorsionForce.h"
#include "openmm/GBSAOBCForce.h"
#include "openmm/GBVIForce.h"
#include "openmm/HarmonicAngleForce.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/LangevinIntegrator.h"
...
...
@@ -78,7 +77,6 @@
#include "openmm/serialization/CustomNonbondedForceProxy.h"
#include "openmm/serialization/CustomTorsionForceProxy.h"
#include "openmm/serialization/GBSAOBCForceProxy.h"
#include "openmm/serialization/GBVIForceProxy.h"
#include "openmm/serialization/HarmonicAngleForceProxy.h"
#include "openmm/serialization/HarmonicBondForceProxy.h"
#include "openmm/serialization/LangevinIntegratorProxy.h"
...
...
@@ -132,7 +130,6 @@ extern "C" void registerSerializationProxies() {
SerializationProxy
::
registerProxy
(
typeid
(
Discrete2DFunction
),
new
Discrete2DFunctionProxy
());
SerializationProxy
::
registerProxy
(
typeid
(
Discrete3DFunction
),
new
Discrete3DFunctionProxy
());
SerializationProxy
::
registerProxy
(
typeid
(
GBSAOBCForce
),
new
GBSAOBCForceProxy
());
SerializationProxy
::
registerProxy
(
typeid
(
GBVIForce
),
new
GBVIForceProxy
());
SerializationProxy
::
registerProxy
(
typeid
(
HarmonicAngleForce
),
new
HarmonicAngleForceProxy
());
SerializationProxy
::
registerProxy
(
typeid
(
HarmonicBondForce
),
new
HarmonicBondForceProxy
());
SerializationProxy
::
registerProxy
(
typeid
(
LangevinIntegrator
),
new
LangevinIntegratorProxy
());
...
...
serialization/tests/TestSerializeGBVIForce.cpp
deleted
100644 → 0
View file @
b20c20fe
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2010-2014 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/GBVIForce.h"
#include "openmm/serialization/XmlSerializer.h"
#include <iostream>
#include <sstream>
using
namespace
OpenMM
;
using
namespace
std
;
void
testSerialization
()
{
// Create a Force.
GBVIForce
force
;
force
.
setForceGroup
(
3
);
force
.
setNonbondedMethod
(
GBVIForce
::
CutoffPeriodic
);
force
.
setBornRadiusScalingMethod
(
GBVIForce
::
QuinticSpline
);
force
.
setQuinticLowerLimitFactor
(
0.123
);
force
.
setQuinticUpperBornRadiusLimit
(
5.123
);
force
.
setCutoffDistance
(
2.0
);
force
.
setSoluteDielectric
(
5.1
);
force
.
setSolventDielectric
(
50.0
);
force
.
addParticle
(
1
,
0.1
,
0.01
);
force
.
addParticle
(
0.5
,
0.2
,
0.02
);
force
.
addParticle
(
-
0.5
,
0.3
,
0.03
);
force
.
addBond
(
0
,
1
,
2.0
);
force
.
addBond
(
3
,
5
,
1.2
);
// Serialize and then deserialize it.
stringstream
buffer
;
XmlSerializer
::
serialize
<
GBVIForce
>
(
&
force
,
"Force"
,
buffer
);
GBVIForce
*
copy
=
XmlSerializer
::
deserialize
<
GBVIForce
>
(
buffer
);
// Compare the two forces to see if they are identical.
GBVIForce
&
force2
=
*
copy
;
ASSERT_EQUAL
(
force
.
getForceGroup
(),
force2
.
getForceGroup
());
ASSERT_EQUAL
(
force
.
getNonbondedMethod
(),
force2
.
getNonbondedMethod
());
ASSERT_EQUAL
(
force
.
getCutoffDistance
(),
force2
.
getCutoffDistance
());
ASSERT_EQUAL
(
force
.
getSoluteDielectric
(),
force2
.
getSoluteDielectric
());
ASSERT_EQUAL
(
force
.
getSolventDielectric
(),
force2
.
getSolventDielectric
());
ASSERT_EQUAL
(
force
.
getNumParticles
(),
force2
.
getNumParticles
());
ASSERT_EQUAL
(
force
.
getQuinticUpperBornRadiusLimit
(),
force2
.
getQuinticUpperBornRadiusLimit
());
ASSERT_EQUAL
(
force
.
getQuinticLowerLimitFactor
(),
force2
.
getQuinticLowerLimitFactor
());
ASSERT_EQUAL
(
force
.
getBornRadiusScalingMethod
(),
force2
.
getBornRadiusScalingMethod
());
for
(
int
i
=
0
;
i
<
force
.
getNumParticles
();
i
++
)
{
double
charge1
,
radius1
,
scale1
;
double
charge2
,
radius2
,
scale2
;
force
.
getParticleParameters
(
i
,
charge1
,
radius1
,
scale1
);
force2
.
getParticleParameters
(
i
,
charge2
,
radius2
,
scale2
);
ASSERT_EQUAL
(
charge1
,
charge2
);
ASSERT_EQUAL
(
radius1
,
radius2
);
ASSERT_EQUAL
(
scale1
,
scale2
);
}
ASSERT_EQUAL
(
force
.
getNumBonds
(),
force2
.
getNumBonds
());
for
(
int
i
=
0
;
i
<
force
.
getNumBonds
();
i
++
)
{
int
a1
,
a2
,
b1
,
b2
;
double
da
,
db
;
force
.
getBondParameters
(
i
,
a1
,
a2
,
da
);
force2
.
getBondParameters
(
i
,
b1
,
b2
,
db
);
ASSERT_EQUAL
(
a1
,
b1
);
ASSERT_EQUAL
(
a2
,
b2
);
ASSERT_EQUAL
(
da
,
db
);
}
}
int
main
()
{
try
{
testSerialization
();
}
catch
(
const
exception
&
e
)
{
cout
<<
"exception: "
<<
e
.
what
()
<<
endl
;
return
1
;
}
cout
<<
"Done"
<<
endl
;
return
0
;
}
wrappers/python/simtk/openmm/app/data/amber03_gbvi.xml
deleted
100644 → 0
View file @
b20c20fe
<ForceField>
<GBVIForce
soluteDielectric=
"1.0"
>
<Atom
type=
"0"
charge=
"0.07601"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1"
charge=
"-0.190263"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"2"
charge=
"0.07601"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"3"
charge=
"0.07601"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"4"
charge=
"0.512403"
radius=
"0.2"
gamma=
"-0.5016616"
/>
<Atom
type=
"5"
charge=
"-0.55017"
radius=
"0.14"
gamma=
"21.2158088"
/>
<Atom
type=
"6"
charge=
"-0.404773"
radius=
"0.165"
gamma=
"-2.6204392"
/>
<Atom
type=
"7"
charge=
"0.294276"
radius=
"0.125"
gamma=
"4.3768824"
/>
<Atom
type=
"8"
charge=
"-0.027733"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"9"
charge=
"0.120802"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"10"
charge=
"-0.229951"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"11"
charge=
"0.077428"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"12"
charge=
"0.570224"
radius=
"0.2"
gamma=
"-0.5016616"
/>
<Atom
type=
"13"
charge=
"-0.555129"
radius=
"0.14"
gamma=
"21.2158088"
/>
<Atom
type=
"14"
charge=
"-0.300879"
radius=
"0.165"
gamma=
"-2.6204392"
/>
<Atom
type=
"15"
charge=
"0.233693"
radius=
"0.125"
gamma=
"4.3768824"
/>
<Atom
type=
"16"
charge=
"-0.131381"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"17"
charge=
"0.053266"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"18"
charge=
"0.036707"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"19"
charge=
"0.028012"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"20"
charge=
"0.012454"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"21"
charge=
"0.002964"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"22"
charge=
"0.126329"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"23"
charge=
"0.068148"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"24"
charge=
"-0.46489"
radius=
"0.165"
gamma=
"-2.6204392"
/>
<Atom
type=
"25"
charge=
"0.326274"
radius=
"0.125"
gamma=
"4.3768824"
/>
<Atom
type=
"26"
charge=
"0.565543"
radius=
"0.2"
gamma=
"-0.5016616"
/>
<Atom
type=
"27"
charge=
"-0.685774"
radius=
"0.165"
gamma=
"-2.6204392"
/>
<Atom
type=
"28"
charge=
"0.391052"
radius=
"0.125"
gamma=
"4.3768824"
/>
<Atom
type=
"29"
charge=
"-0.685774"
radius=
"0.165"
gamma=
"-2.6204392"
/>
<Atom
type=
"30"
charge=
"0.391052"
radius=
"0.125"
gamma=
"4.3768824"
/>
<Atom
type=
"31"
charge=
"0.730308"
radius=
"0.2"
gamma=
"-0.5016616"
/>
<Atom
type=
"32"
charge=
"-0.578332"
radius=
"0.14"
gamma=
"21.2158088"
/>
<Atom
type=
"33"
charge=
"-0.392069"
radius=
"0.165"
gamma=
"-2.6204392"
/>
<Atom
type=
"34"
charge=
"0.282413"
radius=
"0.125"
gamma=
"4.3768824"
/>
<Atom
type=
"35"
charge=
"-0.035317"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"36"
charge=
"0.094292"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"37"
charge=
"-0.121405"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"38"
charge=
"0.069032"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"39"
charge=
"0.67864"
radius=
"0.2"
gamma=
"-0.5016616"
/>
<Atom
type=
"40"
charge=
"-0.55094"
radius=
"0.14"
gamma=
"21.2158088"
/>
<Atom
type=
"41"
charge=
"-0.587163"
radius=
"0.135"
gamma=
"-2.8698056"
/>
<Atom
type=
"42"
charge=
"0.438035"
radius=
"0.1"
gamma=
"9.399356"
/>
<Atom
type=
"43"
charge=
"0.620495"
radius=
"0.2"
gamma=
"-0.5016616"
/>
<Atom
type=
"44"
charge=
"-0.565045"
radius=
"0.14"
gamma=
"21.2158088"
/>
<Atom
type=
"45"
charge=
"-0.430106"
radius=
"0.165"
gamma=
"-2.6204392"
/>
<Atom
type=
"46"
charge=
"0.254543"
radius=
"0.125"
gamma=
"4.3768824"
/>
<Atom
type=
"47"
charge=
"0.044609"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"48"
charge=
"0.059601"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"49"
charge=
"-0.09365"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"50"
charge=
"0.043321"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"51"
charge=
"0.583519"
radius=
"0.2"
gamma=
"-0.5016616"
/>
<Atom
type=
"52"
charge=
"-0.526813"
radius=
"0.14"
gamma=
"21.2158088"
/>
<Atom
type=
"53"
charge=
"-0.781735"
radius=
"0.165"
gamma=
"-2.6204392"
/>
<Atom
type=
"54"
charge=
"0.355079"
radius=
"0.125"
gamma=
"4.3768824"
/>
<Atom
type=
"55"
charge=
"0.617141"
radius=
"0.2"
gamma=
"-0.5016616"
/>
<Atom
type=
"56"
charge=
"-0.523909"
radius=
"0.14"
gamma=
"21.2158088"
/>
<Atom
type=
"57"
charge=
"-0.558201"
radius=
"0.165"
gamma=
"-2.6204392"
/>
<Atom
type=
"58"
charge=
"0.319676"
radius=
"0.125"
gamma=
"4.3768824"
/>
<Atom
type=
"59"
charge=
"0.007225"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"60"
charge=
"0.082375"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"61"
charge=
"-0.047555"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"62"
charge=
"-0.014836"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"63"
charge=
"0.745168"
radius=
"0.2"
gamma=
"-0.5016616"
/>
<Atom
type=
"64"
charge=
"-0.730385"
radius=
"0.14"
gamma=
"21.2158088"
/>
<Atom
type=
"65"
charge=
"-0.730385"
radius=
"0.14"
gamma=
"21.2158088"
/>
<Atom
type=
"66"
charge=
"0.443199"
radius=
"0.2"
gamma=
"-0.5016616"
/>
<Atom
type=
"67"
charge=
"-0.501445"
radius=
"0.14"
gamma=
"21.2158088"
/>
<Atom
type=
"68"
charge=
"-0.4157"
radius=
"0.165"
gamma=
"-2.6204392"
/>
<Atom
type=
"69"
charge=
"0.2719"
radius=
"0.125"
gamma=
"4.3768824"
/>
<Atom
type=
"70"
charge=
"-0.0351"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"71"
charge=
"0.0508"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"72"
charge=
"-0.2413"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"73"
charge=
"0.1122"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"74"
charge=
"-0.8844"
radius=
"0.195"
gamma=
"-4.273956"
/>
<Atom
type=
"75"
charge=
"0.5973"
radius=
"0.2"
gamma=
"-0.5016616"
/>
<Atom
type=
"76"
charge=
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wrappers/python/simtk/openmm/app/data/amber10_gbvi.xml
deleted
100644 → 0
View file @
b20c20fe
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wrappers/python/simtk/openmm/app/data/amber96_gbvi.xml
deleted
100644 → 0
View file @
b20c20fe
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wrappers/python/simtk/openmm/app/data/amber99_gbvi.xml
deleted
100644 → 0
View file @
b20c20fe
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"-2.6204392"
/>
<Atom
type=
"1829"
charge=
"0.4364"
radius=
"0.125"
gamma=
"4.3768824"
/>
<Atom
type=
"1830"
charge=
"-0.6323"
radius=
"0.165"
gamma=
"-2.6204392"
/>
<Atom
type=
"1831"
charge=
"0.1222"
radius=
"0.2"
gamma=
"-0.5016616"
/>
<Atom
type=
"1832"
charge=
"0.2022"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"1833"
charge=
"0.0615"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1834"
charge=
"0.067"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"1835"
charge=
"0.0972"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1836"
charge=
"-0.6139"
radius=
"0.135"
gamma=
"-2.8698056"
/>
<Atom
type=
"1837"
charge=
"0.4186"
radius=
"0.1"
gamma=
"9.399356"
/>
<Atom
type=
"1838"
charge=
"-0.6541"
radius=
"0.135"
gamma=
"-2.8698056"
/>
<Atom
type=
"1839"
charge=
"0.4376"
radius=
"0.1"
gamma=
"9.399356"
/>
<Atom
type=
"1840"
charge=
"1.1662"
radius=
"0.215"
gamma=
"-17.2301304"
/>
<Atom
type=
"1841"
charge=
"-0.776"
radius=
"0.14"
gamma=
"21.2158088"
/>
<Atom
type=
"1842"
charge=
"-0.776"
radius=
"0.14"
gamma=
"21.2158088"
/>
<Atom
type=
"1843"
charge=
"-0.4989"
radius=
"0.135"
gamma=
"-2.8698056"
/>
<Atom
type=
"1844"
charge=
"0.0558"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"1845"
charge=
"0.0679"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1846"
charge=
"0.1065"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"1847"
charge=
"0.1174"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1848"
charge=
"-0.3548"
radius=
"0.135"
gamma=
"-2.8698056"
/>
<Atom
type=
"1849"
charge=
"0.0674"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"1850"
charge=
"0.1824"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1851"
charge=
"0.0418"
radius=
"0.165"
gamma=
"-2.6204392"
/>
<Atom
type=
"1852"
charge=
"-0.1126"
radius=
"0.2"
gamma=
"-0.5016616"
/>
<Atom
type=
"1853"
charge=
"0.2188"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1854"
charge=
"-0.3635"
radius=
"0.2"
gamma=
"-0.5016616"
/>
<Atom
type=
"1855"
charge=
"0.1811"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1856"
charge=
"0.5952"
radius=
"0.2"
gamma=
"-0.5016616"
/>
<Atom
type=
"1857"
charge=
"-0.5761"
radius=
"0.14"
gamma=
"21.2158088"
/>
<Atom
type=
"1858"
charge=
"-0.3549"
radius=
"0.165"
gamma=
"-2.6204392"
/>
<Atom
type=
"1859"
charge=
"0.3154"
radius=
"0.125"
gamma=
"4.3768824"
/>
<Atom
type=
"1860"
charge=
"0.4687"
radius=
"0.2"
gamma=
"-0.5016616"
/>
<Atom
type=
"1861"
charge=
"-0.5477"
radius=
"0.14"
gamma=
"21.2158088"
/>
<Atom
type=
"1862"
charge=
"0.2022"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"1863"
charge=
"0.0615"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1864"
charge=
"0.067"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"1865"
charge=
"0.0972"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1866"
charge=
"-0.6139"
radius=
"0.135"
gamma=
"-2.8698056"
/>
<Atom
type=
"1867"
charge=
"0.4186"
radius=
"0.1"
gamma=
"9.399356"
/>
<Atom
type=
"1868"
charge=
"-0.5246"
radius=
"0.135"
gamma=
"-2.8698056"
/>
<Atom
type=
"1869"
charge=
"1.1662"
radius=
"0.215"
gamma=
"-17.2301304"
/>
<Atom
type=
"1870"
charge=
"-0.776"
radius=
"0.14"
gamma=
"21.2158088"
/>
<Atom
type=
"1871"
charge=
"-0.776"
radius=
"0.14"
gamma=
"21.2158088"
/>
<Atom
type=
"1872"
charge=
"-0.4989"
radius=
"0.135"
gamma=
"-2.8698056"
/>
<Atom
type=
"1873"
charge=
"0.0558"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"1874"
charge=
"0.0679"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1875"
charge=
"0.1065"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"1876"
charge=
"0.1174"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1877"
charge=
"-0.3548"
radius=
"0.135"
gamma=
"-2.8698056"
/>
<Atom
type=
"1878"
charge=
"0.0674"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"1879"
charge=
"0.1824"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1880"
charge=
"0.0418"
radius=
"0.165"
gamma=
"-2.6204392"
/>
<Atom
type=
"1881"
charge=
"-0.1126"
radius=
"0.2"
gamma=
"-0.5016616"
/>
<Atom
type=
"1882"
charge=
"0.2188"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1883"
charge=
"-0.3635"
radius=
"0.2"
gamma=
"-0.5016616"
/>
<Atom
type=
"1884"
charge=
"0.1811"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1885"
charge=
"0.5952"
radius=
"0.2"
gamma=
"-0.5016616"
/>
<Atom
type=
"1886"
charge=
"-0.5761"
radius=
"0.14"
gamma=
"21.2158088"
/>
<Atom
type=
"1887"
charge=
"-0.3549"
radius=
"0.165"
gamma=
"-2.6204392"
/>
<Atom
type=
"1888"
charge=
"0.3154"
radius=
"0.125"
gamma=
"4.3768824"
/>
<Atom
type=
"1889"
charge=
"0.4687"
radius=
"0.2"
gamma=
"-0.5016616"
/>
<Atom
type=
"1890"
charge=
"-0.5477"
radius=
"0.14"
gamma=
"21.2158088"
/>
<Atom
type=
"1891"
charge=
"0.2022"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"1892"
charge=
"0.0615"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1893"
charge=
"0.067"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"1894"
charge=
"0.0972"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1895"
charge=
"-0.6139"
radius=
"0.135"
gamma=
"-2.8698056"
/>
<Atom
type=
"1896"
charge=
"0.4186"
radius=
"0.1"
gamma=
"9.399356"
/>
<Atom
type=
"1897"
charge=
"-0.6541"
radius=
"0.135"
gamma=
"-2.8698056"
/>
<Atom
type=
"1898"
charge=
"0.4376"
radius=
"0.1"
gamma=
"9.399356"
/>
<Atom
type=
"1899"
charge=
"0.4295"
radius=
"0.1"
gamma=
"9.399356"
/>
<Atom
type=
"1900"
charge=
"-0.6223"
radius=
"0.135"
gamma=
"-2.8698056"
/>
<Atom
type=
"1901"
charge=
"0.0558"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"1902"
charge=
"0.0679"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1903"
charge=
"0.1065"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"1904"
charge=
"0.1174"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1905"
charge=
"-0.3548"
radius=
"0.135"
gamma=
"-2.8698056"
/>
<Atom
type=
"1906"
charge=
"0.0674"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"1907"
charge=
"0.1824"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1908"
charge=
"0.0418"
radius=
"0.165"
gamma=
"-2.6204392"
/>
<Atom
type=
"1909"
charge=
"-0.1126"
radius=
"0.2"
gamma=
"-0.5016616"
/>
<Atom
type=
"1910"
charge=
"0.2188"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1911"
charge=
"-0.3635"
radius=
"0.2"
gamma=
"-0.5016616"
/>
<Atom
type=
"1912"
charge=
"0.1811"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1913"
charge=
"0.5952"
radius=
"0.2"
gamma=
"-0.5016616"
/>
<Atom
type=
"1914"
charge=
"-0.5761"
radius=
"0.14"
gamma=
"21.2158088"
/>
<Atom
type=
"1915"
charge=
"-0.3549"
radius=
"0.165"
gamma=
"-2.6204392"
/>
<Atom
type=
"1916"
charge=
"0.3154"
radius=
"0.125"
gamma=
"4.3768824"
/>
<Atom
type=
"1917"
charge=
"0.4687"
radius=
"0.2"
gamma=
"-0.5016616"
/>
<Atom
type=
"1918"
charge=
"-0.5477"
radius=
"0.14"
gamma=
"21.2158088"
/>
<Atom
type=
"1919"
charge=
"0.2022"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"1920"
charge=
"0.0615"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1921"
charge=
"0.067"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"1922"
charge=
"0.0972"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1923"
charge=
"-0.6139"
radius=
"0.135"
gamma=
"-2.8698056"
/>
<Atom
type=
"1924"
charge=
"0.4186"
radius=
"0.1"
gamma=
"9.399356"
/>
<Atom
type=
"1925"
charge=
"-0.5246"
radius=
"0.135"
gamma=
"-2.8698056"
/>
<Atom
type=
"1926"
charge=
"0.4295"
radius=
"0.1"
gamma=
"9.399356"
/>
<Atom
type=
"1927"
charge=
"-0.6223"
radius=
"0.135"
gamma=
"-2.8698056"
/>
<Atom
type=
"1928"
charge=
"0.0558"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"1929"
charge=
"0.0679"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1930"
charge=
"0.1065"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"1931"
charge=
"0.1174"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1932"
charge=
"-0.3548"
radius=
"0.135"
gamma=
"-2.8698056"
/>
<Atom
type=
"1933"
charge=
"0.0674"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"1934"
charge=
"0.1824"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1935"
charge=
"0.0418"
radius=
"0.165"
gamma=
"-2.6204392"
/>
<Atom
type=
"1936"
charge=
"-0.1126"
radius=
"0.2"
gamma=
"-0.5016616"
/>
<Atom
type=
"1937"
charge=
"0.2188"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1938"
charge=
"-0.3635"
radius=
"0.2"
gamma=
"-0.5016616"
/>
<Atom
type=
"1939"
charge=
"0.1811"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1940"
charge=
"0.5952"
radius=
"0.2"
gamma=
"-0.5016616"
/>
<Atom
type=
"1941"
charge=
"-0.5761"
radius=
"0.14"
gamma=
"21.2158088"
/>
<Atom
type=
"1942"
charge=
"-0.3549"
radius=
"0.165"
gamma=
"-2.6204392"
/>
<Atom
type=
"1943"
charge=
"0.3154"
radius=
"0.125"
gamma=
"4.3768824"
/>
<Atom
type=
"1944"
charge=
"0.4687"
radius=
"0.2"
gamma=
"-0.5016616"
/>
<Atom
type=
"1945"
charge=
"-0.5477"
radius=
"0.14"
gamma=
"21.2158088"
/>
<Atom
type=
"1946"
charge=
"0.2022"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"1947"
charge=
"0.0615"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1948"
charge=
"0.067"
radius=
"0.18"
gamma=
"-1.1978792"
/>
<Atom
type=
"1949"
charge=
"0.0972"
radius=
"0.125"
gamma=
"1.0196408"
/>
<Atom
type=
"1950"
charge=
"-0.6139"
radius=
"0.135"
gamma=
"-2.8698056"
/>
<Atom
type=
"1951"
charge=
"0.4186"
radius=
"0.1"
gamma=
"9.399356"
/>
<Atom
type=
"1952"
charge=
"-0.6541"
radius=
"0.135"
gamma=
"-2.8698056"
/>
<Atom
type=
"1953"
charge=
"0.4376"
radius=
"0.1"
gamma=
"9.399356"
/>
</GBVIForce>
</ForceField>
wrappers/python/simtk/openmm/app/forcefield.py
View file @
167ae8a0
...
...
@@ -1393,92 +1393,6 @@ class GBSAOBCGenerator:
parsers
[
"GBSAOBCForce"
]
=
GBSAOBCGenerator
.
parseElement
## @private
class
GBVIGenerator
:
"""A GBVIGenerator constructs a GBVIForce."""
def
__init__
(
self
,
ff
):
self
.
ff
=
ff
self
.
fixedParameters
=
{}
self
.
fixedParameters
[
'soluteDielectric'
]
=
1.0
self
.
fixedParameters
[
'solventDielectric'
]
=
78.3
self
.
fixedParameters
[
'scalingMethod'
]
=
1
self
.
fixedParameters
[
'quinticUpperBornRadiusLimit'
]
=
5.0
self
.
fixedParameters
[
'quinticLowerLimitFactor'
]
=
0.8
self
.
typeMap
=
{}
@
staticmethod
def
parseElement
(
element
,
ff
):
generator
=
GBVIGenerator
(
ff
)
for
key
in
generator
.
fixedParameters
.
iterkeys
():
if
(
key
in
element
.
attrib
):
generator
.
fixedParameters
[
key
]
=
float
(
element
.
attrib
[
key
])
ff
.
registerGenerator
(
generator
)
for
atom
in
element
.
findall
(
'Atom'
):
types
=
ff
.
_findAtomTypes
(
atom
.
attrib
,
1
)
if
None
not
in
types
:
values
=
(
float
(
atom
.
attrib
[
'charge'
]),
float
(
atom
.
attrib
[
'radius'
]),
float
(
atom
.
attrib
[
'gamma'
]))
for
t
in
types
[
0
]:
generator
.
typeMap
[
t
]
=
values
def
createForce
(
self
,
sys
,
data
,
nonbondedMethod
,
nonbondedCutoff
,
args
):
methodMap
=
{
NoCutoff
:
mm
.
NonbondedForce
.
NoCutoff
,
CutoffNonPeriodic
:
mm
.
NonbondedForce
.
CutoffNonPeriodic
,
CutoffPeriodic
:
mm
.
NonbondedForce
.
CutoffPeriodic
}
if
nonbondedMethod
not
in
methodMap
:
raise
ValueError
(
'Illegal nonbonded method for GB/VI Force'
)
# add particles
force
=
mm
.
GBVIForce
()
for
atom
in
data
.
atoms
:
t
=
data
.
atomType
[
atom
]
if
t
in
self
.
typeMap
:
values
=
self
.
typeMap
[
t
]
force
.
addParticle
(
values
[
0
],
values
[
1
],
values
[
2
])
else
:
raise
ValueError
(
'No GB/VI parameters defined for atom type '
+
t
)
# get HarmonicBond generator -- exit if not found
hbGenerator
=
0
for
generator
in
self
.
ff
.
_forces
:
if
(
generator
.
__class__
.
__name__
==
'HarmonicBondGenerator'
):
hbGenerator
=
generator
break
if
(
hbGenerator
==
0
):
raise
ValueError
(
'HarmonicBondGenerator not found.'
)
# add bonds
for
bond
in
data
.
bonds
:
type1
=
data
.
atomType
[
data
.
atoms
[
bond
.
atom1
]]
type2
=
data
.
atomType
[
data
.
atoms
[
bond
.
atom2
]]
for
i
in
range
(
len
(
hbGenerator
.
types1
)):
types1
=
hbGenerator
.
types1
[
i
]
types2
=
hbGenerator
.
types2
[
i
]
if
(
type1
in
types1
and
type2
in
types2
)
or
(
type1
in
types2
and
type2
in
types1
):
#bond.length = hbGenerator.length[i]
force
.
addBond
(
bond
.
atom1
,
bond
.
atom2
,
hbGenerator
.
length
[
i
])
force
.
setNonbondedMethod
(
methodMap
[
nonbondedMethod
])
force
.
setCutoffDistance
(
nonbondedCutoff
)
force
.
setSolventDielectric
(
self
.
fixedParameters
[
'solventDielectric'
])
force
.
setSoluteDielectric
(
self
.
fixedParameters
[
'soluteDielectric'
])
force
.
setBornRadiusScalingMethod
(
self
.
fixedParameters
[
'scalingMethod'
])
force
.
setQuinticLowerLimitFactor
(
self
.
fixedParameters
[
'quinticLowerLimitFactor'
])
force
.
setQuinticUpperBornRadiusLimit
(
self
.
fixedParameters
[
'quinticUpperBornRadiusLimit'
])
sys
.
addForce
(
force
)
parsers
[
"GBVIForce"
]
=
GBVIGenerator
.
parseElement
## @private
class
CustomBondGenerator
:
"""A CustomBondGenerator constructs a CustomBondForce."""
...
...
wrappers/python/simtk/openmm/app/internal/amber_file_parser.py
View file @
167ae8a0
...
...
@@ -674,7 +674,7 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
OPTIONAL ARGUMENTS
shake (String) - if 'h-bonds', will SHAKE all bonds to hydrogen and water; if 'all-bonds', will SHAKE all bonds and water (default: None)
gbmodel (String) - if 'OBC', OBC GBSA will be
used; if 'GBVI', GB/VI will be
used (default: None)
gbmodel (String) - if 'OBC', OBC GBSA will be used (default: None)
soluteDielectric (float) - The solute dielectric constant to use in the implicit solvent model (default: 1.0)
solventDielectric (float) - The solvent dielectric constant to use in the implicit solvent model (default: 78.5)
implicitSolventKappa (float) - The Debye screening parameter corresponding to implicit solvent ionic strength
...
...
@@ -1097,8 +1097,6 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
# created above. Do not bind force to another name before this!
force
.
setReactionFieldDielectric
(
1.0
)
# TODO: Add GBVI terms?
return
system
#=============================================================================================
...
...
wrappers/python/src/swig_doxygen/swigInputConfig.py
View file @
167ae8a0
...
...
@@ -43,7 +43,6 @@ SKIP_METHODS = [('State',),
(
'CalcCustomTorsionForceKernel'
,),
(
'CalcForcesAndEnergyKernel'
,),
(
'CalcGBSAOBCForceKernel'
,),
(
'CalcGBVIForceKernel'
,),
(
'CalcHarmonicAngleForceKernel'
,),
(
'CalcHarmonicBondForceKernel'
,),
(
'CalcKineticEnergyKernel'
,),
...
...
@@ -393,14 +392,6 @@ UNITS = {
:
(
None
,
(
'unit.elementary_charge'
,
'unit.nanometer'
,
None
)),
(
"GBSAOBCForce"
,
"getSurfaceAreaEnergy"
)
:
(
'unit.kilojoule_per_mole/unit.nanometer/unit.nanometer'
,
()),
(
"GBVIForce"
,
"getBornRadiusScalingMethod"
)
:
(
None
,
()),
(
"GBVIForce"
,
"getQuinticLowerLimitFactor"
)
:
(
None
,
()),
(
"GBVIForce"
,
"getQuinticUpperBornRadiusLimit"
)
:
(
'unit.nanometer'
,
()),
(
"GBVIForce"
,
"getBondParameters"
)
:
(
None
,
(
None
,
None
,
'unit.nanometer'
)),
(
"GBVIForce"
,
"getParticleParameters"
)
:
(
None
,
(
'unit.elementary_charge'
,
'unit.nanometer'
,
'unit.kilojoule_per_mole'
)),
(
"HarmonicAngleForce"
,
"getAngleParameters"
)
:
(
None
,
(
None
,
None
,
None
,
'unit.radian'
,
'unit.kilojoule_per_mole/(unit.radian*unit.radian)'
)),
...
...
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