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Commit 73be43c5 authored by peastman's avatar peastman
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Merge pull request #894 from peastman/numadded 

Added option to add a fixed number of solvent molecules
parents 10cc667c bd6ec4b4
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docs-source/usersguide/application.rst
View file @ 73be43c5
......@@ -1405,8 +1405,13 @@ size, you can specify one:
modeller.addSolvent(forcefield, boxSize=Vec3(5.0, 3.5, 3.5)*nanometers)
This requests a 5 nm by 3.5 nm by 3.5 nm box. Another option is to specify a
padding distance:
This requests a 5 nm by 3.5 nm by 3.5 nm box. For a non-rectangular box, you
can specify the three box vectors defining the unit cell:
::
modeller.addSolvent(forcefield, boxVectors=(avec, bvec, cvec))
Another option is to specify a padding distance:
::
modeller.addSolvent(forcefield, padding=1.0*nanometers)
......@@ -1416,6 +1421,14 @@ then creates a cubic box of width (solute size)+2*(padding). The above line
guarantees that no part of the solute comes closer than 1 nm to any edge of the
box.
Finally, you can specify the exact number of solvent molecules (including both
water and ions) to add. This is useful when you want to solvate several different
conformations of the same molecule while guaranteeing they all have the same
amount of solvent:
::
modeller.addSolvent(forcefield, numAdded=5000)
By default, :meth:`addSolvent` creates TIP3P water molecules, but it also supports other
water models:
::
......
wrappers/python/simtk/openmm/app/modeller.py
View file @ 73be43c5
......@@ -240,7 +240,7 @@ class Modeller(object):
self.topology = newTopology
self.positions = newPositions
def addSolvent(self, forcefield, model='tip3p', boxSize=None, boxVectors=None, padding=None, positiveIon='Na+', negativeIon='Cl-', ionicStrength=0*molar):
def addSolvent(self, forcefield, model='tip3p', boxSize=None, boxVectors=None, padding=None, numAdded=None, positiveIon='Na+', negativeIon='Cl-', ionicStrength=0*molar):
"""Add solvent (both water and ions) to the model to fill a rectangular box.
The algorithm works as follows:
......@@ -250,11 +250,15 @@ class Modeller(object):
randomly selecting a water molecule and replacing it with the ion.
4. Ion pairs are added to give the requested total ionic strength.
The box size can be specified in four ways. First, you can explicitly give the vectors defining the periodic box to
use. Alternatively, for a rectangular box you can simply give the dimensions of the unit cell. Third, you can
give a padding distance. The largest dimension of the solute (along the x, y, or z axis) is determined, and a cubic
box of size (largest dimension)+2*padding is used. Finally, if neither box vectors, box size, nor padding distance is specified,
the existing Topology's box vectors are used.
The box size can be specified in any of several ways:
1. You can explicitly give the vectors defining the periodic box to use.
2. Alternatively, for a rectangular box you can simply give the dimensions of the unit cell.
3. You can give a padding distance. The largest dimension of the solute (along the x, y, or z axis) is determined, and a cubic
box of size (largest dimension)+2*padding is used.
4. You can specify the total number of molecules (both waters and ions) to add. A cubic box is then created whose size is
just large enough hold the specified amount of solvent.
5. Finally, if none of the above options is specified, the existing Topology's box vectors are used.
Parameters:
- forcefield (ForceField) the ForceField to use for determining van der Waals radii and atomic charges
......@@ -262,14 +266,43 @@ class Modeller(object):
- boxSize (Vec3=None) the size of the box to fill with water
- boxVectors (tuple of Vec3=None) the vectors defining the periodic box to fill with water
- padding (distance=None) the padding distance to use
- numAdded (int=None) the total number of molecules (waters and ions) to add
- positiveIon (string='Na+') the type of positive ion to add. Allowed values are 'Cs+', 'K+', 'Li+', 'Na+', and 'Rb+'
- negativeIon (string='Cl-') the type of negative ion to add. Allowed values are 'Cl-', 'Br-', 'F-', and 'I-'. Be aware
that not all force fields support all ion types.
- ionicStrength (concentration=0*molar) the total concentration of ions (both positive and negative) to add. This
does not include ions that are added to neutralize the system.
"""
if len([x for x in (boxSize, boxVectors, padding, numAdded) if x is not None]) > 1:
raise ValueError('At most one of the following arguments may be specified: boxSize, boxVectors, padding, numAdded')
# Load the pre-equilibrated water box.
vdwRadiusPerSigma = 0.5612310241546864907
if model == 'tip3p':
waterRadius = 0.31507524065751241*vdwRadiusPerSigma
elif model == 'spce':
waterRadius = 0.31657195050398818*vdwRadiusPerSigma
elif model == 'tip4pew':
waterRadius = 0.315365*vdwRadiusPerSigma
elif model == 'tip5p':
waterRadius = 0.312*vdwRadiusPerSigma
else:
raise ValueError('Unknown water model: %s' % model)
pdb = PDBFile(os.path.join(os.path.dirname(__file__), 'data', model+'.pdb'))
pdbTopology = pdb.getTopology()
pdbPositions = pdb.getPositions().value_in_unit(nanometer)
pdbResidues = list(pdbTopology.residues())
pdbBoxSize = pdbTopology.getUnitCellDimensions().value_in_unit(nanometer)
# Pick a unit cell size.
if numAdded is not None:
# Select a padding distance which is guaranteed to give more than the specified number of molecules.
padding = 1.1*(numAdded/((len(pdbResidues)/pdbBoxSize[0]**3)*8))**(1.0/3.0)
if padding < 0.5:
padding = 0.5 # Ensure we have enough when adding very small numbers of molecules
if boxVectors is not None:
if is_quantity(boxVectors[0]):
boxVectors = (boxVectors[0].value_in_unit(nanometer), boxVectors[1].value_in_unit(nanometer), boxVectors[2].value_in_unit(nanometer))
......@@ -305,25 +338,6 @@ class Modeller(object):
positiveElement = posIonElements[positiveIon]
negativeElement = negIonElements[negativeIon]
# Load the pre-equilibrated water box.
vdwRadiusPerSigma = 0.5612310241546864907
if model == 'tip3p':
waterRadius = 0.31507524065751241*vdwRadiusPerSigma
elif model == 'spce':
waterRadius = 0.31657195050398818*vdwRadiusPerSigma
elif model == 'tip4pew':
waterRadius = 0.315365*vdwRadiusPerSigma
elif model == 'tip5p':
waterRadius = 0.312*vdwRadiusPerSigma
else:
raise ValueError('Unknown water model: %s' % model)
pdb = PDBFile(os.path.join(os.path.dirname(__file__), 'data', model+'.pdb'))
pdbTopology = pdb.getTopology()
pdbPositions = pdb.getPositions().value_in_unit(nanometer)
pdbResidues = list(pdbTopology.residues())
pdbBoxSize = pdbTopology.getUnitCellDimensions().value_in_unit(nanometer)
# Have the ForceField build a System for the solute from which we can determine van der Waals radii.
system = forcefield.createSystem(self.topology)
......@@ -424,27 +438,42 @@ class Modeller(object):
addedWaters.append((residue.index, atomPos))
# There could be clashes between water molecules at the box edges. Find ones to remove.
upperCutoff = center+box/2-Vec3(waterCutoff, waterCutoff, waterCutoff)
lowerCutoff = center-box/2+Vec3(waterCutoff, waterCutoff, waterCutoff)
lowerSkinPositions = [pos for index, pos in addedWaters if pos[0] < lowerCutoff[0] or pos[1] < lowerCutoff[1] or pos[2] < lowerCutoff[2]]
filteredWaters = []
cells = {}
for i in range(len(lowerSkinPositions)):
cell = tuple((int(floor(lowerSkinPositions[i][j]/cellSize[j]))%numCells[j] for j in range(3)))
if cell in cells:
cells[cell].append(i)
else:
cells[cell] = [i]
for entry in addedWaters:
pos = entry[1]
if pos[0] < upperCutoff[0] and pos[1] < upperCutoff[1] and pos[2] < upperCutoff[2]:
filteredWaters.append(entry)
else:
if not any((periodicDistance(lowerSkinPositions[i], pos) < waterCutoff and norm(lowerSkinPositions[i]-pos) > waterCutoff for i in neighbors(pos))):
if numAdded is not None:
# We added many more waters than we actually want. Sort them based on distance to the nearest box edge and
# only keep the ones in the middle.
lowerBound = center-box/2
upperBound = center+box/2
distToEdge = (min(min(pos-lowerBound), min(upperBound-pos)) for index, pos in addedWaters)
sortedIndex = [i[0] for i in sorted(enumerate(distToEdge), key=lambda x: -x[1])]
addedWaters = [addedWaters[i] for i in sortedIndex[:numAdded]]
# Compute a new periodic box size.
maxSize = max(max((pos[i] for index, pos in addedWaters))-min((pos[i] for index, pos in addedWaters)) for i in range(3))
newTopology.setUnitCellDimensions(Vec3(maxSize, maxSize, maxSize))
else:
# There could be clashes between water molecules at the box edges. Find ones to remove.
upperCutoff = center+box/2-Vec3(waterCutoff, waterCutoff, waterCutoff)
lowerCutoff = center-box/2+Vec3(waterCutoff, waterCutoff, waterCutoff)
lowerSkinPositions = [pos for index, pos in addedWaters if pos[0] < lowerCutoff[0] or pos[1] < lowerCutoff[1] or pos[2] < lowerCutoff[2]]
filteredWaters = []
cells = {}
for i in range(len(lowerSkinPositions)):
cell = tuple((int(floor(lowerSkinPositions[i][j]/cellSize[j]))%numCells[j] for j in range(3)))
if cell in cells:
cells[cell].append(i)
else:
cells[cell] = [i]
for entry in addedWaters:
pos = entry[1]
if pos[0] < upperCutoff[0] and pos[1] < upperCutoff[1] and pos[2] < upperCutoff[2]:
filteredWaters.append(entry)
addedWaters = filteredWaters
else:
if not any((periodicDistance(lowerSkinPositions[i], pos) < waterCutoff and norm(lowerSkinPositions[i]-pos) > waterCutoff for i in neighbors(pos))):
filteredWaters.append(entry)
addedWaters = filteredWaters
# Add ions to neutralize the system.
......
wrappers/python/tests/TestModeller.py
View file @ 73be43c5
......@@ -308,7 +308,7 @@ class TestModeller(unittest.TestCase):
self.assertTrue(len(matoms)==0 and len(m1atoms)==1 and len(m2atoms)==1)
def test_addSolventPeriodicBox(self):
""" Test the addSolvent() method; test that the four ways of passing in the periodic box all work. """
""" Test the addSolvent() method; test that the five ways of passing in the periodic box all work. """
# First way of passing in periodic box vectors: set it in the original topology.
topology_start = self.pdb.topology
......@@ -358,6 +358,14 @@ class TestModeller(unittest.TestCase):
self.assertVecAlmostEqual(dim3[0]/nanometers, Vec3(2.8802, 0, 0))
self.assertVecAlmostEqual(dim3[1]/nanometers, Vec3(0, 2.8802, 0))
self.assertVecAlmostEqual(dim3[2]/nanometers, Vec3(0, 0, 2.8802))
# Fifth way: specify a number of molecules to add instead of a box size
topology_start = self.pdb.topology
modeller = Modeller(topology_start, self.positions)
modeller.deleteWater()
numInitial = len(list(modeller.topology.residues()))
modeller.addSolvent(self.forcefield, numAdded=1000)
self.assertEqual(numInitial+1000, len(list(modeller.topology.residues())))
def test_addSolventNeutralSolvent(self):
""" Test the addSolvent() method; test adding ions to neutral solvent. """
......@@ -389,7 +397,7 @@ class TestModeller(unittest.TestCase):
def test_addSolventNegativeSolvent(self):
""" Test the addSolvent() method; test adding ions to a negatively charged solvent. """
topology_start = self.pdb.topology
topology_start.setUnitCellDimensions(Vec3(3.5, 3.5, 3.5)*nanometers)
......@@ -476,7 +484,7 @@ class TestModeller(unittest.TestCase):
topology_start = self.pdb.topology
topology_start.setUnitCellDimensions(Vec3(3.5, 3.5, 3.5)*nanometers)
# set up modeller with no solvent
modeller = Modeller(topology_start, self.positions)
modeller.deleteWater()
......@@ -490,7 +498,7 @@ class TestModeller(unittest.TestCase):
modeller = Modeller(topology_nowater, positions_nowater)
modeller.addSolvent(self.forcefield, positiveIon=positiveIon, ionicStrength=1.0*molar)
topology_after = modeller.getTopology()
water_count = 0
positive_ion_count = 0
chlorine_count = 0
......@@ -514,7 +522,7 @@ class TestModeller(unittest.TestCase):
modeller.addSolvent(self.forcefield, negativeIon=negativeIon, ionicStrength=1.0*molar)
topology_after = modeller.getTopology()
water_count = 0
sodium_count = 0
negative_ion_count = 0
......@@ -543,7 +551,7 @@ class TestModeller(unittest.TestCase):
# remove hydrogens from the topology
toDelete = [atom for atom in topology_start.atoms() if atom.element==Element.getBySymbol('H')]
modeller.delete(toDelete)
# Create a variants list to force the one histidine to be of the right variation.
residues = [residue for residue in topology_start.residues()]
variants = [None]*len(residues)
......@@ -557,7 +565,7 @@ class TestModeller(unittest.TestCase):
topology_after = modeller.getTopology()
validate_equivalence(self, topology_start, topology_after)
def test_addHydrogensPdb3(self):
""" Test the addHydrogens() method on the metallothionein pdb file. """
......@@ -650,7 +658,7 @@ class TestModeller(unittest.TestCase):
# There should be extra hydrogens on the CYS residues. Assert that they exist
# on modeller2, then delete them and validate that the topologies match.
# These are the indices of the hydrogens to delete from CYS to make CYX.
index_list_CYS = [31, 49, 110, 135, 171, 193, 229]
atoms = [atom for atom in topology2.atoms()]
......
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