Merge branch 'master' into feature/cuda-docker

wrappers/python/simtk/openmm/app/pdbfile.py

@@ -352,9 +352,11 @@ class PDBFile(object):
                     resName = res.name
                 if keepIds and len(res.id) < 5:
                     resId = res.id
-                    resIC = res.insertionCode
                 else:
                     resId = "%4d" % ((resIndex+1)%10000)
+                if len(res.insertionCode) == 1:
+                    resIC = res.insertionCode
+                else:
                     resIC = " "
                 if res.name in nonHeterogens:
                     recordName = "ATOM  "

wrappers/python/simtk/openmm/app/simulatedtempering.py

+from __future__ import print_function
+
+"""
+simulatedtempering.py: Implements simulated tempering
+
+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) 2015 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.
+"""
+__author__ = "Peter Eastman"
+__version__ = "1.0"
+
+import simtk.unit as unit
+import math
+import random
+from sys import stdout
+
+try:
+    import bz2
+    have_bz2 = True
+except: have_bz2 = False
+
+try:
+    import gzip
+    have_gzip = True
+except: have_gzip = False
+
+class SimulatedTempering(object):
+    """SimulatedTempering implements the simulated tempering algorithm for accelerated sampling.
+    
+    It runs a simulation while allowing the temperature to vary.  At high temperatures, it can more easily cross
+    energy barriers to explore a wider area of conformation space.  At low temperatures, it can thoroughly
+    explore each local region.  For details, see Marinari, E. and Parisi, G., Europhys. Lett. 19(6). pp. 451-458 (1992).
+    
+    The set of temperatures to sample can be specified in two ways.  First, you can explicitly provide a list
+    of temperatures by using the "temperatures" argument.  Alternatively, you can specify the minimum and
+    maximum temperatures, and the total number of temperatures to use.  The temperatures are chosen spaced
+    exponentially between the two extremes.  For example,
+    
+    st = SimulatedTempering(simulation, numTemperatures=15, minTemperature=300*kelvin, maxTemperature=450*kelvin)
+    
+    After creating the SimulatedTempering object, call step() on it to run the simulation.
+    
+    Transitions between temperatures are performed at regular intervals, as specified by the "tempChangeInterval"
+    argument.  For each transition, a new temperature is selected using the independence sampling method, as
+    described in Chodera, J. and Shirts, M., J. Chem. Phys. 135, 194110 (2011).
+    
+    Simulated tempering requires a "weight factor" for each temperature.  Ideally, these should be chosen so
+    the simulation spends equal time at every temperature.  You can specify the list of weights to use with the
+    optional "weights" argument.  If this is omitted, weights are selected automatically using the Wang-Landau
+    algorithm as described in Wang, F. and Landau, D. P., Phys. Rev. Lett. 86(10), pp. 2050-2053 (2001).
+    
+    To properly analyze the results of the simulation, it is important to know the temperature and weight factors
+    at every point in time.  The SimulatedTempering object functions as a reporter, writing this information
+    to a file or stdout at regular intervals (which should match the interval at which you save frames from the
+    simulation).  You can specify the output file and reporting interval with the "reportFile" and "reportInterval"
+    arguments.
+    """
+
+    def __init__(self, simulation, temperatures=None, numTemperatures=None, minTemperature=None, maxTemperature=None, weights=None, tempChangeInterval=25, reportInterval=1000, reportFile=stdout):
+        """Create a new SimulatedTempering.
+        
+        Parameters
+        ----------
+        simulation: Simulation
+            The Simulation defining the System, Context, and Integrator to use
+        temperatures: list
+            The list of temperatures to use for tempering, in increasing order
+        numTemperatures: int
+            The number of temperatures to use for tempering.  If temperatures is not None, this is ignored.
+        minTemperature: temperature
+            The minimum temperature to use for tempering.  If temperatures is not None, this is ignored.
+        maxTemperature: temperature
+            The maximum temperature to use for tempering.  If temperatures is not None, this is ignored.
+        weights: list
+            The weight factor for each temperature.  If none, weights are selected automatically.
+        tempChangeInterval: int
+            The interval (in time steps) at which to attempt transitions between temperatures
+        reportInterval: int
+            The interval (in time steps) at which to write information to the report file
+        reportFile: string or file
+            The file to write reporting information to, specified as a file name or file object
+        """        
+        self.simulation = simulation
+        if temperatures is None:
+            if unit.is_quantity(minTemperature):
+                minTemperature = minTemperature.value_in_unit(unit.kelvin)
+            if unit.is_quantity(maxTemperature):
+                maxTemperature = maxTemperature.value_in_unit(unit.kelvin)
+            self.temperatures = [minTemperature*((float(maxTemperature)/minTemperature)**(i/float(numTemperatures-1))) for i in range(numTemperatures)]*unit.kelvin
+        else:
+            numTemperatures = len(temperatures)
+            self.temperatures = [(t.value_in_unit(unit.kelvin) if unit.is_quantity(t) else t)*unit.kelvin for t in temperatures]
+            if any(self.temperatures[i] >= self.temperatures[i+1] for i in range(numTemperatures-1)):
+                raise ValueError('The temperatures must be in strictly increasing order')
+        self.tempChangeInterval = tempChangeInterval
+        self.reportInterval = reportInterval
+        self.inverseTemperatures = [1.0/(unit.MOLAR_GAS_CONSTANT_R*t) for t in self.temperatures]
+
+        # If necessary, open the file we will write reports to.
+
+        self._openedFile = isinstance(reportFile, str)
+        if self._openedFile:
+            # Detect the desired compression scheme from the filename extension
+            # and open all files unbuffered
+            if reportFile.endswith('.gz'):
+                if not have_gzip:
+                    raise RuntimeError("Cannot write .gz file because Python could not import gzip library")
+                self._out = gzip.GzipFile(fileobj=open(reportFile, 'wb', 0))
+            elif reportFile.endswith('.bz2'):
+                if not have_bz2:
+                    raise RuntimeError("Cannot write .bz2 file because Python could not import bz2 library")
+                self._out = bz2.BZ2File(reportFile, 'w', 0)
+            else:
+                self._out = open(reportFile, 'w', 1)
+        else:
+            self._out = reportFile
+        
+        # Initialize the weights.
+        
+        if weights is None:
+            self._weights = [0.0]*numTemperatures
+            self._updateWeights = True
+            self._weightUpdateFactor = 1.0
+            self._histogram = [0]*numTemperatures
+            self._hasMadeTransition = False
+        else:
+            self._weights = weights
+            self._updateWeights = False
+
+        # Select the initial temperature.
+        
+        self.currentTemperature = 0
+        self.simulation.integrator.setTemperature(self.temperatures[self.currentTemperature])
+        
+        # Add a reporter to the simulation which will handle the updates and reports.
+        
+        class STReporter(object):
+            def __init__(self, st):
+                self.st = st
+
+            def describeNextReport(self, simulation):
+                st = self.st
+                steps1 = st.tempChangeInterval - simulation.currentStep%st.tempChangeInterval
+                steps2 = st.reportInterval - simulation.currentStep%st.reportInterval
+                steps = min(steps1, steps2)
+                isUpdateAttempt = (steps1 == steps)
+                return (steps, False, isUpdateAttempt, False, isUpdateAttempt)
+
+            def report(self, simulation, state):
+                st = self.st
+                if simulation.currentStep%st.tempChangeInterval == 0:
+                    st._attemptTemperatureChange(state)
+                if simulation.currentStep%st.reportInterval == 0:
+                    st._writeReport()
+        
+        simulation.reporters.append(STReporter(self))
+        
+        # Write out the header line.
+        
+        headers = ['Steps', 'Temperature (K)']
+        for t in self.temperatures:
+            headers.append('%gK Weight' % t.value_in_unit(unit.kelvin))
+        print('#"%s"' % ('"\t"').join(headers), file=self._out)
+
+    def __del__(self):
+        if self._openedFile:
+            self._out.close()
+    
+    @property
+    def weights(self):
+        return [x-self._weights[0] for x in self._weights]
+
+    def step(self, steps):
+        """Advance the simulation by integrating a specified number of time steps."""
+        self.simulation.step(steps)
+    
+    def _attemptTemperatureChange(self, state):
+        """Attempt to move to a different temperature."""
+        
+        # Compute the probability for each temperature.  This is done in log space to avoid overflow.
+
+        logProbability = [(self._weights[i]-self.inverseTemperatures[i]*state.getPotentialEnergy()) for i in range(len(self._weights))]
+        maxLogProb = max(logProbability)
+        offset = maxLogProb + math.log(sum(math.exp(x-maxLogProb) for x in logProbability))
+        probability = [math.exp(x-offset) for x in logProbability]
+        r = random.random()
+        for j in range(len(probability)):
+            if r < probability[j]:
+                if j != self.currentTemperature:
+                    # Rescale the velocities.
+                    
+                    scale = math.sqrt(self.temperatures[j]/self.temperatures[self.currentTemperature])
+                    velocities = [v*scale for v in state.getVelocities().value_in_unit(unit.nanometers/unit.picoseconds)]
+                    self.simulation.context.setVelocities(velocities)
+
+                    # Select this temperature.
+                    
+                    self._hasMadeTransition = True
+                    self.currentTemperature = j
+                    self.simulation.integrator.setTemperature(self.temperatures[j])
+                if self._updateWeights:
+                    # Update the weight factors.
+                    
+                    self._weights[j] -= self._weightUpdateFactor
+                    self._histogram[j] += 1
+                    minCounts = min(self._histogram)
+                    if minCounts > 20 and minCounts >= 0.2*sum(self._histogram)/len(self._histogram):
+                        # Reduce the weight update factor and reset the histogram.
+                        
+                        self._weightUpdateFactor *= 0.5
+                        self._histogram = [0]*len(self.temperatures)
+                        self._weights = [x-self._weights[0] for x in self._weights]
+                    elif not self._hasMadeTransition and probability[self.currentTemperature] > 0.99:
+                        # Rapidly increase the weight update factor at the start of the simulation to find
+                        # a reasonable starting value.
+                        
+                        self._weightUpdateFactor *= 2.0
+                        self._histogram = [0]*len(self.temperatures)
+                return
+            r -= probability[j]
+
+    def _writeReport(self):
+        """Write out a line to the report."""
+        temperature = self.temperatures[self.currentTemperature].value_in_unit(unit.kelvin)
+        values = [temperature]+self.weights
+        print(('%d\t' % self.simulation.currentStep) + '\t'.join('%g' % v for v in values), file=self._out)

wrappers/python/tests/TestAmberPrmtopFile.py

@@ -127,6 +127,14 @@ class TestAmberPrmtopFile(unittest.TestCase):
                     self.assertTrue(found_matching_solvent_dielectric and
                                     found_matching_solute_dielectric)
 
+    def test_ImplicitSolventZeroSA(self):
+        """Test that requesting gbsaModel=None yields a surface area energy of 0 when 
+           prmtop.createSystem produces a GBSAOBCForce"""
+        system = prmtop2.createSystem(implicitSolvent=OBC2, gbsaModel=None)
+        for force in system.getForces():
+            if isinstance(force, GBSAOBCForce):
+                self.assertEqual(force.getSurfaceAreaEnergy(), 0*kilojoule/(nanometer**2*mole))
+
     def test_HydrogenMass(self):
         """Test that altering the mass of hydrogens works correctly."""
 

wrappers/python/tests/TestCharmmFiles.py

@@ -93,12 +93,10 @@ class TestCharmmFiles(unittest.TestCase):
     def test_NBFIX(self):
         """Tests CHARMM systems with NBFIX Lennard-Jones modifications"""
         warnings.filterwarnings('ignore', category=CharmmPSFWarning)
-        psf = CharmmPsfFile('systems/ala3_solv.psf')
+        psf = CharmmPsfFile('systems/ala3_solv.psf', unitCellDimensions=Vec3(32.7119500, 32.9959600, 33.0071500)*angstroms)
         crd = CharmmCrdFile('systems/ala3_solv.crd')
         params = CharmmParameterSet('systems/par_all36_prot.prm',
                                     'systems/toppar_water_ions.str')
-        # Box dimensions (found from bounding box)
-        psf.setBox(32.7119500*angstroms, 32.9959600*angstroms, 33.0071500*angstroms)
 
         # Turn off charges so we only test the Lennard-Jones energies
         for a in psf.atom_list:
@@ -114,7 +112,7 @@ class TestCharmmFiles(unittest.TestCase):
 
         state = con.getState(getEnergy=True, enforcePeriodicBox=True)
         ene = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
-        self.assertAlmostEqual(ene, 15490.0033559, delta=0.05)
+        self.assertAlmostEqual(ene, 15559.71602, delta=0.05)
 
     def test_Drude(self):
         """Test CHARMM systems with Drude force field"""
@@ -127,14 +125,14 @@ class TestCharmmFiles(unittest.TestCase):
 
         # Now compute the full energy
         plat = Platform.getPlatformByName('Reference')
-        system = psf.createSystem(params, nonbondedMethod=PME)
+        system = psf.createSystem(params, nonbondedMethod=PME, ewaldErrorTolerance=0.00005)
         integrator = DrudeLangevinIntegrator(300*kelvin, 1.0/picosecond, 1*kelvin, 10/picosecond, 0.001*picoseconds)
         con = Context(system, integrator, plat)
         con.setPositions(crd.positions)
 
         state = con.getState(getEnergy=True, enforcePeriodicBox=True)
         ene = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
-        self.assertAlmostEqual(ene, -1831.54, delta=0.5)
+        self.assertAlmostEqual(ene, -1788.36644, delta=1.0)
 
     def test_Lonepair(self):
         """Test the lonepair facilities, in particular the colinear type of lonepairs"""
@@ -169,12 +167,11 @@ class TestCharmmFiles(unittest.TestCase):
     def testSystemOptions(self):
         """ Test various options in CharmmPsfFile.createSystem """
         warnings.filterwarnings('ignore', category=CharmmPSFWarning)
-        psf = CharmmPsfFile('systems/ala3_solv.psf')
+        psf = CharmmPsfFile('systems/ala3_solv.psf',
+                            periodicBoxVectors=(Vec3(32.7119500, 0, 0)*angstroms, Vec3(0, 32.9959600, 0)*angstroms, Vec3(0, 0, 33.0071500)*angstroms))
         crd = CharmmCrdFile('systems/ala3_solv.crd')
         params = CharmmParameterSet('systems/par_all36_prot.prm',
                                     'systems/toppar_water_ions.str')
-        # Box dimensions (found from bounding box)
-        psf.setBox(32.7119500*angstroms, 32.9959600*angstroms, 33.0071500*angstroms)
 
         # Check some illegal options
         self.assertRaises(ValueError, lambda:
@@ -275,6 +272,58 @@ class TestCharmmFiles(unittest.TestCase):
                     dtheta = math.pi-angle
                 self.assertAlmostEqual(energy, dtheta**2, delta=1e-5)
 
+    def test_Residues(self):
+        """Test that residues are read correctly, even if they have the same RESID while being in separate segments."""
+        m14 = (["C{}".format(i) for i in range(1,14)]
+               + ["H{}".format(i) for i in range(1,12)]
+               + ["N{}".format(i) for i in range(1,4)]
+               )
+        tip3 = ["OH2", "H1", "H2"]
+        pot = ["POT"]
+        cla = ["CLA"]
+        psf = CharmmPsfFile('systems/charmm-solvated/isa_wat.3_kcl.m14.psf')
+        for residue in psf.topology.residues():
+            atoms = [atom.name for atom in residue.atoms()]
+            if residue.name == "M14":
+                self.assertEqual(sorted(m14), sorted(atoms))
+            elif residue.name == "TIP3":
+                self.assertEqual(sorted(tip3), sorted(atoms))
+            elif residue.name == "POT":
+                self.assertEqual(sorted(pot), sorted(atoms))
+            elif residue.name == "CLA":
+                self.assertEqual(sorted(cla), sorted(atoms))
+            else:
+                self.assertTrue(False)
+
+    def test_NoLongRangeCorrection(self):
+        """Test that long range correction is disabled."""
+        parameters = CharmmParameterSet(
+            'systems/charmm-solvated/envi.str',
+            'systems/charmm-solvated/m14.rtf',
+            'systems/charmm-solvated/m14.prm'
+        )
+        psf = CharmmPsfFile('systems/charmm-solvated/isa_wat.3_kcl.m14.psf')
+        psf.setBox(3.0584*nanometers,3.0584*nanometers,3.0584*nanometers)
+        system = psf.createSystem(parameters, nonbondedMethod=PME)
+        for force in system.getForces():
+            if isinstance(force, CustomNonbondedForce):
+                self.assertFalse(force.getUseLongRangeCorrection())
+            if isinstance(force, NonbondedForce):
+                self.assertFalse(force.getUseDispersionCorrection())
+
+    def test_NoPsfWarning(self):
+        """Test that PSF warning is not thrown."""
+        parameters = CharmmParameterSet(
+            'systems/charmm-solvated/envi.str',
+            'systems/charmm-solvated/m14.rtf',
+            'systems/charmm-solvated/m14.prm'
+        )
+        with warnings.catch_warnings():
+            warnings.simplefilter("error", CharmmPSFWarning)
+            psf = CharmmPsfFile('systems/charmm-solvated/isa_wat.3_kcl.m14.psf')
+            psf.setBox(3.0584*nanometers,3.0584*nanometers,3.0584*nanometers)
+            psf.createSystem(parameters, nonbondedMethod=PME)
+
 
 if __name__ == '__main__':
     unittest.main()

wrappers/python/tests/TestForceField.py

@@ -6,6 +6,7 @@ from simtk.unit import *
 import simtk.openmm.app.element as elem
 import simtk.openmm.app.forcefield as forcefield
 import math
+import textwrap
 try:
     from cStringIO import StringIO
 except ImportError:
@@ -50,16 +51,77 @@ class TestForceField(unittest.TestCase):
                                 for f in forces))
 
     def test_DispersionCorrection(self):
-        """Test to make sure the nonbondedCutoff parameter is passed correctly."""
-
-        for useDispersionCorrection in [True, False]:
-            system = self.forcefield1.createSystem(self.pdb1.topology,
-                                                   nonbondedCutoff=2*nanometer,
-                                                   useDispersionCorrection=useDispersionCorrection)
+        """Test to make sure that the dispersion/long-range correction is set properly."""
+        top = Topology()
+        chain = top.addChain()
 
+        for lrc in (True, False):
+            xml = textwrap.dedent(
+                """
+                <ForceField>
+                 <LennardJonesForce lj14scale="0.3" useDispersionCorrection="{lrc}">
+                  <Atom type="A" sigma="1" epsilon="0.1"/>
+                  <Atom type="B" sigma="2" epsilon="0.2"/>
+                  <NBFixPair type1="A" type2="B" sigma="2.5" epsilon="1.1"/>
+                 </LennardJonesForce>
+                 <NonbondedForce coulomb14scale="0.833333" lj14scale="0.5" useDispersionCorrection="{lrc2}">
+                  <Atom type="A" sigma="0.315" epsilon="0.635"/>
+                 </NonbondedForce>
+                </ForceField>
+                """
+            )
+            ff = ForceField(StringIO(xml.format(lrc=lrc, lrc2=lrc)))
+            system = ff.createSystem(top)
+            checked_nonbonded = False
+            checked_custom = False
             for force in system.getForces():
                 if isinstance(force, NonbondedForce):
-                    self.assertEqual(useDispersionCorrection, force.getUseDispersionCorrection())
+                    self.assertEqual(force.getUseDispersionCorrection(), lrc)
+                    checked_nonbonded = True
+                elif isinstance(force, CustomNonbondedForce):
+                    self.assertEqual(force.getUseLongRangeCorrection(), lrc)
+                    checked_custom = True
+            self.assertTrue(checked_nonbonded and checked_custom)
+
+            # check that the keyword argument overwrites xml input
+            lrc_kwarg = not lrc
+            with warnings.catch_warnings(record=True) as w:
+                warnings.simplefilter("always")
+                system2 = ff.createSystem(top, useDispersionCorrection=lrc_kwarg)
+                self.assertTrue(len(w) == 2)
+                assert "conflict" in str(w[-1].message).lower()
+            checked_nonbonded = False
+            checked_custom = False
+            for force in system2.getForces():
+                if isinstance(force, NonbondedForce):
+                    self.assertEqual(force.getUseDispersionCorrection(), lrc_kwarg)
+                    checked_nonbonded = True
+                elif isinstance(force, CustomNonbondedForce):
+                    self.assertEqual(force.getUseLongRangeCorrection(), lrc_kwarg)
+                    checked_custom = True
+            self.assertTrue(checked_nonbonded and checked_custom)
+
+            # check that no warning is generated when useDispersionCorrection is not in the xml file
+            xml = textwrap.dedent(
+                """
+                <ForceField>
+                 <LennardJonesForce lj14scale="0.3">
+                  <Atom type="A" sigma="1" epsilon="0.1"/>
+                  <Atom type="B" sigma="2" epsilon="0.2"/>
+                  <NBFixPair type1="A" type2="B" sigma="2.5" epsilon="1.1"/>
+                 </LennardJonesForce>
+                 <NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
+                  <Atom type="A" sigma="0.315" epsilon="0.635"/>
+                 </NonbondedForce>
+                </ForceField>
+                """
+            )
+            ff = ForceField(StringIO(xml))
+            system = ff.createSystem(top)
+            for lrc_kwarg in [True, False]:
+                with warnings.catch_warnings():
+                    warnings.simplefilter("error")
+                    system2 = ff.createSystem(top, useDispersionCorrection=lrc_kwarg)
 
     def test_Cutoff(self):
         """Test to make sure the nonbondedCutoff parameter is passed correctly."""
@@ -227,7 +289,7 @@ class TestForceField(unittest.TestCase):
         angles = forcefield.HarmonicAngleGenerator(ff)
         angles.registerAngle({'class1':'HW', 'class2':'OW', 'class3':'HW', 'angle':1.82421813418*radians, 'k':836.8*kilojoules_per_mole/radian})
         ff.registerGenerator(angles)
-        nonbonded = forcefield.NonbondedGenerator(ff, 0.833333, 0.5)
+        nonbonded = forcefield.NonbondedGenerator(ff, 0.833333, 0.5, True)
         nonbonded.registerAtom({'type':'tip3p-O', 'charge':-0.834, 'sigma':0.31507524065751241*nanometers, 'epsilon':0.635968*kilojoules_per_mole})
         nonbonded.registerAtom({'type':'tip3p-H', 'charge':0.417, 'sigma':1*nanometers, 'epsilon':0*kilojoules_per_mole})
         ff.registerGenerator(nonbonded)
@@ -712,7 +774,7 @@ class TestForceField(unittest.TestCase):
    <Atom name="SOD" type="SOD"/>
   </Residue>
  </Residues>
- <LennardJonesForce lj14scale="1.0">
+ <LennardJonesForce lj14scale="1.0" useDispersionCorrection="False">
   <Atom type="CLA" sigma="0.404468018036" epsilon="0.6276"/>
   <Atom type="SOD" sigma="0.251367073323" epsilon="0.1962296"/>
   <NBFixPair type1="CLA" type2="SOD" sigma="0.33239431" epsilon="0.350933"/>
@@ -940,5 +1002,6 @@ class AmoebaTestForceField(unittest.TestCase):
             diff = norm(f1-f2)
             self.assertTrue(diff < 0.1 or diff/norm(f1) < 1e-3)
 
+
 if __name__ == '__main__':
     unittest.main()

wrappers/python/tests/TestMetadynamics.py

+import unittest
+from simtk.openmm import *
+from simtk.openmm.app import *
+from simtk.unit import *
+
+class TestMetadynamics(unittest.TestCase):
+    """Test the Metadynamics class"""
+
+    def testHarmonicOscillator(self):
+        """Test running metadynamics on a harmonic oscillator."""
+        system = System()
+        system.addParticle(1.0)
+        system.addParticle(1.0)
+        force = HarmonicBondForce()
+        force.addBond(0, 1, 1.0, 100000.0)
+        system.addForce(force)
+        cv = CustomBondForce('r')
+        cv.addBond(0, 1)
+        bias = BiasVariable(cv, 0.94, 1.06, 0.02)
+        meta = Metadynamics(system, [bias], 300*kelvin, 2.0, 5.0, 10)
+        integrator = LangevinIntegrator(300*kelvin, 10/picosecond, 0.001*picosecond)
+        topology = Topology()
+        chain = topology.addChain()
+        residue = topology.addResidue('H2', chain)
+        topology.addAtom('H1', element.hydrogen, residue)
+        topology.addAtom('H2', element.hydrogen, residue)
+        simulation = Simulation(topology, system, integrator, Platform.getPlatformByName('Reference'))
+        simulation.context.setPositions([Vec3(0, 0, 0), Vec3(1, 0, 0)])
+        meta.step(simulation, 200000)
+        fe = meta.getFreeEnergy()
+        center = bias.gridWidth//2
+        fe -= fe[center]
+
+        # Energies should be reasonably well converged over the central part of the range.
+
+        for i in range(center-3, center+4):
+            r = bias.minValue + i*(bias.maxValue-bias.minValue)/(bias.gridWidth-1)
+            e = 0.5*100000.0*(r-1.0)**2*kilojoules_per_mole
+            assert abs(fe[i]-e) < 1.0*kilojoules_per_mole
\ No newline at end of file

wrappers/python/tests/TestSimulatedTempering.py

+import unittest
+from simtk.openmm import *
+from simtk.openmm.app import *
+from simtk.unit import *
+
+class TestSimulatedTempering(unittest.TestCase):
+    """Test the SimulatedTempering class"""
+
+    def testHarmonicOscillator(self):
+        """Test running simulated tempering on a harmonic oscillator."""
+        system = System()
+        system.addParticle(1.0)
+        system.addParticle(1.0)
+        force = HarmonicBondForce()
+        force.addBond(0, 1, 1.0, 1000.0)
+        system.addForce(force)
+        integrator = LangevinIntegrator(300*kelvin, 10/picosecond, 0.001*picosecond)
+        topology = Topology()
+        chain = topology.addChain()
+        residue = topology.addResidue('H2', chain)
+        topology.addAtom('H1', element.hydrogen, residue)
+        topology.addAtom('H2', element.hydrogen, residue)
+        simulation = Simulation(topology, system, integrator, Platform.getPlatformByName('Reference'))
+        st = SimulatedTempering(simulation, numTemperatures=10, minTemperature=200*kelvin, maxTemperature=400*kelvin, tempChangeInterval=5, reportInterval=10000)
+        self.assertEqual(10, len(st.temperatures))
+        self.assertEqual(200*kelvin, st.temperatures[0])
+        self.assertEqual(400*kelvin, st.temperatures[-1])
+        simulation.context.setPositions([Vec3(0, 0, 0), Vec3(1, 0, 0)])
+        
+        # Run for a little while to let the weights stabilize.
+        
+        st.step(10000)
+        
+        # Run for a while and record the temperatures and distances.
+        
+        distances = [[] for i in range(10)]
+        count = 0
+        for i in range(7000):
+            st.step(5)
+            pos = simulation.context.getState(getPositions=True).getPositions().value_in_unit(nanometers)
+            r = norm(pos[0]-pos[1])
+            distances[st.currentTemperature].append(r)
+            count += 1
+
+        # Check that it spent roughly equal time at each temperature, and that the distributions
+        # are correct.
+
+        for d, t in zip(distances, st.temperatures):
+            n = len(d)
+            assert count/20 < n < count/5
+            meanDist = sum(d)/n
+            assert 0.97 < meanDist < 1.03
+            meanEnergy = sum([0.5*1000*(r-1)**2 for r in d])/n
+            expectedEnergy = (0.5*MOLAR_GAS_CONSTANT_R*t).value_in_unit(kilojoules_per_mole)
+            self.assertAlmostEqual(expectedEnergy, meanEnergy, delta=expectedEnergy*0.3)
\ No newline at end of file

wrappers/python/tests/systems/charmm-solvated/envi.str

+* STREAM FILE FOR ENVIRONMENT
+*
+
+set nat ?NATC
+set app
+!We're exploiting what is arguably a bug in the parser. On the left hand side,
+!the quotes have priority, so NAT is correctly substituted. On the right hand
+!side, the ? has priority and NATC" (sic) is not a valid substitution...
+if "@NAT" ne "?NATC" if @nat ne 0 set app append
+
+
+READ RTF CARD @{app}
+* Constructed Based on Stream File from CGenff
+*
+36 1
+
+MASS  -1  CCX2     12.01100  C
+MASS  -1  HCX2      1.00800  H
+MASS  -1  OCX1     15.99940  O
+MASS  -1  HOX1      1.00800  H
+MASS  -1  CCX3     12.01100  C
+MASS  -1  HCX3      1.00800  H
+MASS  -1   HT       1.00800  H 
+MASS  -1   OT      15.99940  O 
+MASS  -1  CLA      35.45000  CL
+MASS  -1  POT      39.09830  K 
+
+DEFA FIRS NONE LAST NONE
+AUTO ANGLES DIHE DRUDE
+
+RESI OCOH     0.000 ! PARAM_PENALTY=0.0000 ; CHARGE_PENALTY=0.0000
+GROUP            ! CHARGE   CH_PENALTY
+ATOM C1     CCX2    0.050 !    0.000
+ATOM H11    HCX2    0.090 !    0.000
+ATOM H12    HCX2    0.090 !    0.000
+ATOM O1     OCX1   -0.649 !    0.000
+ATOM HO1    HOX1    0.420 !    0.000
+ATOM C2     CCX2   -0.181 !    0.000
+ATOM H21    HCX2    0.090 !    0.000
+ATOM H22    HCX2    0.090 !    0.000
+ATOM C3     CCX2   -0.180 !    0.000
+ATOM H31    HCX2    0.090 !    0.000
+ATOM H32    HCX2    0.090 !    0.000
+ATOM C4     CCX2   -0.180 !    0.000
+ATOM H41    HCX2    0.090 !    0.000
+ATOM H42    HCX2    0.090 !    0.000
+ATOM C5     CCX2   -0.180 !    0.000
+ATOM H51    HCX2    0.090 !    0.000
+ATOM H52    HCX2    0.090 !    0.000
+ATOM C6     CCX2   -0.180 !    0.000
+ATOM H61    HCX2    0.090 !    0.000
+ATOM H62    HCX2    0.090 !    0.000
+ATOM C7     CCX2   -0.180 !    0.000
+ATOM H71    HCX2    0.090 !    0.000
+ATOM H72    HCX2    0.090 !    0.000
+ATOM C8     CCX3   -0.270 !    0.000
+ATOM H81    HCX3    0.090 !    0.000
+ATOM H82    HCX3    0.090 !    0.000
+ATOM H83    HCX3    0.090 !    0.000
+
+BOND H12  C1  
+BOND H31  C3  
+BOND H51  C5  
+BOND H71  C7  
+BOND H42  C4  
+BOND H22  C2  
+BOND H62  C6  
+BOND H82  C8  
+BOND C1   H11 
+BOND C1   C2  
+BOND C1   O1  
+BOND C3   C2  
+BOND C3   C4  
+BOND C3   H32 
+BOND C5   C4  
+BOND C5   C6  
+BOND C5   H52 
+BOND C7   C6  
+BOND C7   C8  
+BOND C7   H72 
+BOND H83  C8  
+BOND C2   H21 
+BOND C4   H41 
+BOND C6   H61 
+BOND C8   H81 
+BOND HO1  O1  
+
+RESI TIP3         0.000 
+GROUP
+ATOM OH2  OT     -0.834
+ATOM H1   HT      0.417
+ATOM H2   HT      0.417
+BOND OH2 H1 OH2 H2 H1 H2    ! the last bond is needed for shake
+ANGLE H1 OH2 H2             ! required
+DONOR H1 OH2
+DONOR H2 OH2
+ACCEPTOR OH2
+PATCHING FIRS NONE LAST NONE
+
+RESI POT       1.00 ! Potassium Ion
+GROUP
+ATOM POT   POT 1.00
+PATCHING FIRST NONE LAST NONE
+
+RESI CLA      -1.00 ! Chloride Ion
+GROUP
+ATOM CLA  CLA -1.00
+PATCHING FIRST NONE LAST NONE
+
+END
+
+READ PARA CARD FLEX @{APP}
+* PARAMETERS FOR ENVIR
+*
+
+
+ATOMS
+MASS  -1  CCX2     12.01100 ! CGENFF_PRM
+MASS  -1  HCX2      1.00800 ! CGENFF_PRM
+MASS  -1  OCX1     15.99940 ! CGENFF_PRM
+MASS  -1  HOX1      1.00800 ! CGENFF_PRM
+MASS  -1  CCX3     12.01100 ! CGENFF_PRM
+MASS  -1  HCX3      1.00800 ! CGENFF_PRM
+MASS  -1  HT        1.00800 ! CGENFF_PRM 
+MASS  -1  OT       15.99940 ! CGENFF_PRM
+MASS  -1  CLA      35.45000 ! CGENFF_PRM
+MASS  -1  POT      39.09830 ! CGENFF_PRM
+
+
+BONDS
+CCX2  CCX2    222.500    1.5300 ! CGENFF_PRM
+CCX2  CCX3    222.500    1.5280 ! CGENFF_PRM
+CCX2  OCX1    428.000    1.4200 ! CGENFF_PRM
+CCX2  HCX2    309.000    1.1110 ! CGENFF_PRM
+CCX3  HCX3    322.000    1.1110 ! CGENFF_PRM
+OCX1  HOX1    545.000    0.9600 ! CGENFF_PRM
+HT    HT        0.0      1.5139 ! CGENFF_PRM
+HT    OT      450.000    0.9572 ! CGENFF_PRM
+
+ANGLES
+CCX2   CCX2   CCX2     58.350   113.6000    11.160   2.5610 ! CGENFF_PRM
+CCX2   CCX2   CCX3     58.000   115.0000     8.000   2.5610 ! CGENFF_PRM
+CCX2   CCX2   OCX1     75.700   110.1000 ! CGENFF_PRM
+CCX2   CCX2   HCX2     26.500   110.1000    22.530   2.1790 ! CGENFF_PRM
+CCX3   CCX2   HCX2     34.600   110.1000    22.530   2.1790 ! CGENFF_PRM
+OCX1   CCX2   HCX2     45.900   108.8900 ! CGENFF_PRM
+HCX2   CCX2   HCX2     35.500   109.0000     5.400   1.8020 ! CGENFF_PRM
+CCX2   CCX3   HCX3     34.600   110.1000    22.530   2.1790 ! CGENFF_PRM
+HCX3   CCX3   HCX3     35.500   108.4000     5.400   1.8020 ! CGENFF_PRM
+CCX2   OCX1   HOX1     50.000   106.0000 ! CGENFF_PRM
+HT     OT     HT       55.000   104.5200 ! CGENFF_PRM   
+
+DIHEDRALS
+CCX2  CCX2  CCX2  CCX2      0.0645  2    0.00 ! CGENFF_PRM
+CCX2  CCX2  CCX2  CCX2      0.1497  3  180.00 ! CGENFF_PRM
+CCX2  CCX2  CCX2  CCX2      0.0946  4    0.00 ! CGENFF_PRM
+CCX2  CCX2  CCX2  CCX2      0.1125  5    0.00 ! CGENFF_PRM
+CCX2  CCX2  CCX2  CCX3      0.1505  2    0.00 ! CGENFF_PRM
+CCX2  CCX2  CCX2  CCX3      0.0813  3  180.00 ! CGENFF_PRM
+CCX2  CCX2  CCX2  CCX3      0.1082  4    0.00 ! CGENFF_PRM
+CCX2  CCX2  CCX2  CCX3      0.2039  5    0.00 ! CGENFF_PRM
+CCX2  CCX2  CCX2  OCX1      0.1950  3    0.00 ! CGENFF_PRM
+CCX2  CCX2  CCX2  HCX2      0.1950  3    0.00 ! CGENFF_PRM
+CCX3  CCX2  CCX2  HCX2      0.1800  3    0.00 ! CGENFF_PRM
+OCX1  CCX2  CCX2  HCX2      0.1950  3    0.00 ! CGENFF_PRM
+HCX2  CCX2  CCX2  HCX2      0.2200  3    0.00 ! CGENFF_PRM
+CCX2  CCX2  CCX3  HCX3      0.1600  3    0.00 ! CGENFF_PRM
+HCX2  CCX2  CCX3  HCX3      0.1600  3    0.00 ! CGENFF_PRM
+CCX2  CCX2  OCX1  HOX1      1.1300  1    0.00 ! CGENFF_PRM
+CCX2  CCX2  OCX1  HOX1      0.1400  2    0.00 ! CGENFF_PRM
+CCX2  CCX2  OCX1  HOX1      0.2400  3    0.00 ! CGENFF_PRM
+HCX2  CCX2  OCX1  HOX1      0.1800  3    0.00 ! CGENFF_PRM
+
+IMPROPERS
+
+NONBONDED nbxmod  5 atom cdiel fshift vatom vdistance vfswitch -
+cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
+CCX2    0.0      -0.0560   2.0100  0.0  -0.0100  1.9000 ! CGENFF_PRM
+HCX2    0.0      -0.0350   1.3400 ! CGENFF_PRM
+OCX1    0.0      -0.1921   1.7650 ! CGENFF_PRM
+HOX1    0.0      -0.0460   0.2245 ! CGENFF_PRM
+CCX3    0.0      -0.0780   2.0500  0.0  -0.0100  1.9000 ! CGENFF_PRM
+HCX3    0.0      -0.0240   1.3400 ! CGENFF_PRM
+HT       0.0     -0.0460   0.2245 ! CGENFF_PRM
+OT       0.0     -0.1521   1.7682 ! CGENFF_PRM
+POT      0.0     -0.0870   1.76375 ! CGENFF_PRM 
+CLA      0.0     -0.1500   2.27    ! CGENFF_PRM
+
+
+NBFIX
+POT    CLA      -0.114236   4.081 ! CGENFF_PRM 
+
+HBOND CUTHB 0.5
+
+END
+

wrappers/python/tests/systems/charmm-solvated/m14.prm

+* PRM File generated from CGenFF STR
+*
+
+ATOMS
+MASS  -1  NG2S3    14.00700 ! CGENFF_PRM
+MASS  -1  CG2R61   12.01100 ! CGENFF_PRM
+MASS  -1  CG2RC0   12.01100 ! CGENFF_PRM
+MASS  -1  NG2R50   14.00700 ! CGENFF_PRM
+MASS  -1  CG2R53   12.01100 ! CGENFF_PRM
+MASS  -1  NG2R51   14.00700 ! CGENFF_PRM
+MASS  -1  HGP4      1.00800 ! CGENFF_PRM
+MASS  -1  HGR61     1.00800 ! CGENFF_PRM
+MASS  -1  HGR52     1.00800 ! CGENFF_PRM
+
+BONDS
+CG2R53 NG2R50  400.000    1.3200 ! CGENFF_PRM
+CG2R53 NG2R51  320.000    1.3740 ! CGENFF_PRM
+CG2R53 HGR52   340.000    1.0900 ! CGENFF_PRM
+CG2R61 CG2R61  305.000    1.3750 ! CGENFF_PRM
+CG2R61 CG2RC0  300.000    1.3600 ! CGENFF_PRM
+CG2R61 NG2R51  400.000    1.4200 ! CGENFF_PRM
+CG2R61 NG2S3   400.000    1.3900 ! CGENFF_PRM
+CG2R61 HGR61   340.000    1.0800 ! CGENFF_PRM
+CG2RC0 CG2RC0  360.000    1.3850 ! CGENFF_PRM
+CG2RC0 NG2R50  310.000    1.3650 ! CGENFF_PRM
+CG2RC0 NG2R51  300.000    1.3750 ! CGENFF_PRM
+NG2S3  HGP4    488.000    1.0000 ! CGENFF_PRM
+
+ANGLES
+NG2R50 CG2R53 NG2R51  100.000   113.0000 ! CGENFF_PRM
+NG2R50 CG2R53 HGR52    39.000   124.8000 ! CGENFF_PRM
+NG2R51 CG2R53 HGR52    40.000   122.2000 ! CGENFF_PRM
+CG2R61 CG2R61 CG2R61   40.000   120.0000    35.000   2.4162 ! CGENFF_PRM
+CG2R61 CG2R61 CG2RC0   50.000   120.0000 ! CGENFF_PRM
+CG2R61 CG2R61 NG2R51   60.000   121.0000 ! CGENFF_PRM
+CG2R61 CG2R61 NG2S3    60.000   121.0000 ! CGENFF_PRM
+CG2R61 CG2R61 HGR61    30.000   120.0000    22.000   2.1525 ! CGENFF_PRM
+CG2RC0 CG2R61 HGR61    30.000   120.0000    22.000   2.1460 ! CGENFF_PRM
+CG2R61 CG2RC0 CG2RC0   50.000   120.0000 ! CGENFF_PRM
+CG2R61 CG2RC0 NG2R50  130.000   130.0000 ! CGENFF_PRM
+CG2R61 CG2RC0 NG2R51  130.000   132.6000 ! CGENFF_PRM
+CG2RC0 CG2RC0 NG2R50  100.000   110.0000 ! CGENFF_PRM
+CG2RC0 CG2RC0 NG2R51  100.000   105.7000 ! CGENFF_PRM
+CG2R53 NG2R50 CG2RC0  120.000   103.8000 ! CGENFF_PRM
+CG2R53 NG2R51 CG2R61   40.000   127.0000 ! PENALTY= 2.5
+CG2R53 NG2R51 CG2RC0  100.000   107.2000 ! CGENFF_PRM
+CG2R61 NG2R51 CG2RC0   40.000   127.0000 ! PENALTY= 1.0
+CG2R61 NG2S3  HGP4     60.000   111.6000 ! CGENFF_PRM
+HGP4   NG2S3  HGP4     31.000   117.0000 ! CGENFF_PRM
+
+DIHEDRALS
+NG2R51 CG2R53 NG2R50 CG2RC0   14.0000  2  180.00 ! CGENFF_PRM
+HGR52  CG2R53 NG2R50 CG2RC0    5.2000  2  180.00 ! CGENFF_PRM
+NG2R50 CG2R53 NG2R51 CG2R61    6.0000  2  180.00 ! PENALTY= 47.5
+NG2R50 CG2R53 NG2R51 CG2RC0    6.0000  2  180.00 ! CGENFF_PRM
+HGR52  CG2R53 NG2R51 CG2R61    0.0000  2  180.00 ! PENALTY= 32.0
+HGR52  CG2R53 NG2R51 CG2RC0    5.6000  2  180.00 ! CGENFF_PRM
+CG2R61 CG2R61 CG2R61 CG2R61    3.1000  2  180.00 ! CGENFF_PRM
+CG2R61 CG2R61 CG2R61 CG2RC0    3.0000  2  180.00 ! CGENFF_PRM
+CG2R61 CG2R61 CG2R61 NG2R51    5.0000  2  180.00 ! CGENFF_PRM
+CG2R61 CG2R61 CG2R61 NG2S3     5.0000  2  180.00 ! CGENFF_PRM
+CG2R61 CG2R61 CG2R61 HGR61     4.2000  2  180.00 ! CGENFF_PRM
+CG2RC0 CG2R61 CG2R61 NG2S3     5.0000  2  180.00 ! PENALTY= 1.5
+CG2RC0 CG2R61 CG2R61 HGR61     3.0000  2  180.00 ! CGENFF_PRM
+NG2R51 CG2R61 CG2R61 HGR61     2.4000  2  180.00 ! CGENFF_PRM
+NG2S3  CG2R61 CG2R61 HGR61     2.4000  2  180.00 ! CGENFF_PRM
+HGR61  CG2R61 CG2R61 HGR61     2.4000  2  180.00 ! CGENFF_PRM
+CG2R61 CG2R61 CG2RC0 CG2RC0    3.0000  2  180.00 ! CGENFF_PRM
+CG2R61 CG2R61 CG2RC0 NG2R50    1.5000  2  180.00 ! CGENFF_PRM
+CG2R61 CG2R61 CG2RC0 NG2R51    3.0000  2  180.00 ! CGENFF_PRM
+HGR61  CG2R61 CG2RC0 CG2RC0    3.0000  2  180.00 ! CGENFF_PRM
+HGR61  CG2R61 CG2RC0 NG2R50    0.8000  2  180.00 ! CGENFF_PRM
+HGR61  CG2R61 CG2RC0 NG2R51    3.0000  2  180.00 ! CGENFF_PRM
+CG2R61 CG2R61 NG2R51 CG2R53    0.2000  1    0.00 ! PENALTY= 2.5
+CG2R61 CG2R61 NG2R51 CG2R53    1.1000  2  180.00 ! PENALTY= 2.5
+CG2R61 CG2R61 NG2R51 CG2R53    0.6000  3    0.00 ! PENALTY= 2.5
+CG2R61 CG2R61 NG2R51 CG2RC0    0.2000  1    0.00 ! PENALTY= 1.0
+CG2R61 CG2R61 NG2R51 CG2RC0    1.1000  2  180.00 ! PENALTY= 1.0
+CG2R61 CG2R61 NG2R51 CG2RC0    0.6000  3    0.00 ! PENALTY= 1.0
+CG2R61 CG2R61 NG2S3  HGP4      1.3500  2  180.00 ! CGENFF_PRM
+CG2R61 CG2RC0 CG2RC0 CG2R61    3.0000  2  180.00 ! CGENFF_PRM
+CG2R61 CG2RC0 CG2RC0 NG2R50    1.5000  2  180.00 ! CGENFF_PRM
+CG2R61 CG2RC0 CG2RC0 NG2R51    1.5000  2  180.00 ! CGENFF_PRM
+NG2R50 CG2RC0 CG2RC0 NG2R51   10.0000  2  180.00 ! CGENFF_PRM
+CG2R61 CG2RC0 NG2R50 CG2R53   15.0000  2  180.00 ! CGENFF_PRM
+CG2RC0 CG2RC0 NG2R50 CG2R53    6.0000  2  180.00 ! CGENFF_PRM
+CG2R61 CG2RC0 NG2R51 CG2R53   19.0000  2  180.00 ! CGENFF_PRM
+CG2R61 CG2RC0 NG2R51 CG2R61    0.5000  2  180.00 ! PENALTY= 47.5
+CG2RC0 CG2RC0 NG2R51 CG2R53    6.0000  2  180.00 ! CGENFF_PRM
+CG2RC0 CG2RC0 NG2R51 CG2R61    1.5000  2  180.00 ! PENALTY= 49.0
+
+IMPROPERS
+NG2S3  HGP4   HGP4   CG2R61   -2.5000  0    0.00 ! CGENFF_PRM
+
+NONBONDED nbxmod  5 atom cdiel fshift vatom vdistance vfswitch -
+cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
+NG2S3   0.0      -0.2000   1.8500 ! CGENFF_PRM
+CG2R61  0.0      -0.0700   1.9924 ! CGENFF_PRM
+CG2RC0  0.0      -0.0990   1.8600 ! CGENFF_PRM
+NG2R50  0.0      -0.2000   1.8500 ! CGENFF_PRM
+CG2R53  0.0      -0.0200   2.2000 ! CGENFF_PRM
+NG2R51  0.0      -0.2000   1.8500 ! CGENFF_PRM
+HGP4    0.0      -0.0460   0.2245 ! CGENFF_PRM
+HGR61   0.0      -0.0300   1.3582 ! CGENFF_PRM
+HGR52   0.0      -0.0460   0.9000 ! CGENFF_PRM
+
+NBFIX
+
+HBOND CUTHB 0.5
+
+END
\ No newline at end of file

wrappers/python/tests/systems/charmm-solvated/m14.rtf

+* Constructed Based on Stream File from CGenff
+*
+36 1
+
+MASS  -1  NG2S3    14.00700  N
+MASS  -1  CG2R61   12.01100  C
+MASS  -1  CG2RC0   12.01100  C
+MASS  -1  NG2R50   14.00700  N
+MASS  -1  CG2R53   12.01100  C
+MASS  -1  NG2R51   14.00700  N
+MASS  -1  HGP4      1.00800  H
+MASS  -1  HGR61     1.00800  H
+MASS  -1  HGR52     1.00800  H
+
+DEFA FIRS NONE LAST NONE
+AUTO ANGLES DIHE DRUDE
+
+RESI M14      0.000 ! PARAM_PENALTY=49.0000 ; CHARGE_PENALTY=28.5710
+GROUP            ! CHARGE   CH_PENALTY
+ATOM N1     NG2S3  -0.838 !    0.620
+ATOM C1     CG2R61  0.004 !    0.598
+ATOM C2     CG2R61 -0.190 !    0.000
+ATOM C3     CG2R61 -0.328 !   21.664
+ATOM C4     CG2RC0  0.099 !   21.730
+ATOM C5     CG2RC0  0.474 !    1.670
+ATOM N2     NG2R50 -0.717 !    2.375
+ATOM C6     CG2R53  0.130 !   25.244
+ATOM N3     NG2R51  0.090 !   28.571
+ATOM C7     CG2R61  0.109 !   27.814
+ATOM C8     CG2R61 -0.116 !    0.851
+ATOM C9     CG2R61 -0.115 !    0.000
+ATOM C10    CG2R61 -0.115 !    0.000
+ATOM C11    CG2R61 -0.115 !    0.000
+ATOM C12    CG2R61 -0.116 !    0.851
+ATOM C13    CG2R61 -0.367 !    0.598
+ATOM H1     HGP4    0.382 !    0.000
+ATOM H2     HGP4    0.382 !    0.000
+ATOM H3     HGR61   0.196 !    0.000
+ATOM H4     HGR61   0.195 !    0.000
+ATOM H5     HGR52   0.131 !   12.362
+ATOM H6     HGR61   0.115 !    0.000
+ATOM H7     HGR61   0.115 !    0.000
+ATOM H8     HGR61   0.115 !    0.000
+ATOM H9     HGR61   0.115 !    0.000
+ATOM H10    HGR61   0.115 !    0.000
+ATOM H11    HGR61   0.250 !    0.000
+
+BOND N1   C1  
+BOND N1   H1  
+BOND N1   H2  
+BOND C1   C13 
+BOND C1   C2  
+BOND C2   C3  
+BOND C2   H3  
+BOND C3   C4  
+BOND C3   H4  
+BOND C4   N3  
+BOND C4   C5  
+BOND C5   N2  
+BOND C5   C13 
+BOND N2   C6  
+BOND C6   H5  
+BOND C6   N3  
+BOND N3   C7  
+BOND C7   C8  
+BOND C7   C12 
+BOND C8   H6  
+BOND C8   C9  
+BOND C9   H7  
+BOND C9   C10 
+BOND C10  H8  
+BOND C10  C11 
+BOND C11  C12 
+BOND C11  H9  
+BOND C12  H10 
+BOND C13  H11 
+IMPR N1    H2    H1    C1  
+
+
+END

wrappers/python/tests/systems/ions.pdb

 CRYST1   12.009   12.338   11.510  90.00  90.00  90.00 P 1
 ATOM      1  SOD SOD I   1      -5.844   1.432   3.239  1.00  0.00      ION NA
-ATOM      2  CLA CLA I   2      -5.605  -3.153   1.213  1.00  0.00      ION CL
+ATOM      2  CLA CLA I   2      -5.605  -1.153   1.213  1.00  0.00      ION CL
 END
\ No newline at end of file