def test_load_parmed():
top_fname = fn("tz2.ortho.parm7")
traj_fname = fn("tz2.ortho.nc")
parm = parmed.load_file(top_fname, xyz=traj_fname)
traj = pt.load_parmed(parm, traj=True)
aa_eq(parm.get_coordinates(), traj.xyz)
aa_eq(parm.box, traj.top.box.tolist())
aa_eq(parm.get_box(), traj.unitcells)
def static_DAT_restraint(
restraint_mask_list,
num_window_list,
ref_structure,
force_constant,
continuous_apr=True,
amber_index=False,
):
"""
Create a restraint whose value does not change during a calculation.
Parameters
----------
restraint_mask_list: list
A list of masks for which this restraint applies.
num_window_list: list
A list of windows during which this restraint will be applied, which should be in the form: [attach windows,
pull windows, release windows].
ref_structure: Path-like or parmed Amber object
The reference structure that is used to determine the initial, **static** value for this restraint.
force_constant: float
The force constant for this restraint.
continuous_apr: bool
Whether this restraint uses ``continuous_apr``. This must be consistent with existing restraints.
amber_index: bool
Whether the atom indices for the restraint should be AMBER-style (+1) or not.
Returns
-------
rest: ``DAT_restraint``
A static restraint.
"""
# Check num_window_list
if len(num_window_list) != 3:
raise ValueError(
"The num_window_list needs to contain three integers corresponding to the number of windows in the "
"attach, pull, and release phase, respectively ")
rest = DAT_restraint()
rest.continuous_apr = continuous_apr
rest.amber_index = amber_index
if isinstance(ref_structure, pmd.amber._amberparm.AmberParm):
reference_trajectory = pt.load_parmed(ref_structure, traj=True)
rest.topology = ref_structure
elif isinstance(ref_structure, str):
reference_trajectory = pt.iterload(ref_structure, traj=True)
rest.topology = pmd.load_file(ref_structure, structure=True)
else:
raise TypeError(
"static_DAT_restraint does not support the type associated with ref_structure:"
+ type(ref_structure))
rest.mask1 = restraint_mask_list[0]
rest.mask2 = restraint_mask_list[1]
if len(restraint_mask_list) >= 3:
rest.mask3 = restraint_mask_list[2]
if len(restraint_mask_list) == 4:
rest.mask4 = restraint_mask_list[3]
# Target value
mask_string = " ".join(restraint_mask_list)
if len(restraint_mask_list) == 2:
# Distance restraint
if reference_trajectory.top.has_box():
target = pt.distance(reference_trajectory, mask_string,
image=True)[0]
logger.debug("Calculating distance with 'image = True' ...")
else:
target = pt.distance(reference_trajectory,
mask_string,
image=False)[0]
logger.debug("Calculating distance with 'image = False' ...")
elif len(restraint_mask_list) == 3:
# Angle restraint
target = pt.angle(reference_trajectory, mask_string)[0]
elif len(restraint_mask_list) == 4:
# Dihedral restraint
target = pt.dihedral(reference_trajectory, mask_string)[0]
else:
raise IndexError(
f"The number of masks -- {len(restraint_mask_list)} -- is not 2, 3, or 4 and thus is not one of the "
f"supported types: distance, angle, or dihedral.")
# Attach phase
if num_window_list[0] is not None and num_window_list[0] != 0:
rest.attach["target"] = target
rest.attach["fc_initial"] = force_constant
rest.attach["fc_final"] = force_constant
rest.attach["num_windows"] = num_window_list[0]
# Pull phase
if num_window_list[1] is not None and num_window_list[1] != 0:
rest.pull["fc"] = force_constant
rest.pull["target_initial"] = target
rest.pull["target_final"] = target
rest.pull["num_windows"] = num_window_list[1]
# Release phase
if num_window_list[2] is not None and num_window_list[2] != 0:
rest.release["target"] = target
rest.release["fc_initial"] = force_constant
rest.release["fc_final"] = force_constant
rest.release["num_windows"] = num_window_list[2]
rest.initialize()
return rest
#Also, first frame in trajectory is NOT at time zero, so subtract 1
if endTime == -1:
thisPot = alcDat[:, 3:-1]
else:
thisPot = alcDat[:endTime, 3:-1]
thisg = timeseries.statisticalInefficiencyMultiple(thisPot)
print("Statistical inefficiency for this set of potential energies: %f" %
thisg)
#print(startTime)
#print(startFrame)
#print(thisPot.shape)
#Next load in the trajectory and get all solute coordinates that matter
top.rb_torsions = pmd.TrackedList([])
top = pt.load_parmed(top, traj=False)
if endTime == -1:
traj = pt.iterload(trajFile, top, frame_slice=(startFrame, -1))
else:
traj = pt.iterload(trajFile,
top,
frame_slice=(startFrame, startFrame + endTime))
nFrames = len(traj)
xyBox = np.array(
traj[0].box.values
)[:
2] #A little lazy, but all boxes should be same and fixed in X and Y dimensions
#print(nFrames)
#To correctly map solute positions on both sides of surface, need fixed reference on each surface face
def getConfigWeightsSurf(kB=0.008314459848, T=298.15):
"""Computes and returns the configuration weights for simulations with a solute
at an interface.
Mostly replicates calcdGsolv in genetic_lib, but returns config weights in both
the fully coupled and decoupled states (also includes pV term - won't matter very
much for free energy differences, but maybe matters for weighting configurations,
even though also probably not too much).
"""
#First define directory structure, spring constants, etc.
simDirs = ['Quad_0.25X_0.25Y', 'Quad_0.25X_0.75Y', 'Quad_0.75X_0.25Y', 'Quad_0.75X_0.75Y']
kXY = [10.0, 10.0, 10.0, 10.0] #spring constant in kJ/mol*A^2
refX = [7.4550, 7.4550, 22.3650, 22.3650]
refY = [8.6083, 25.8249, 8.6083, 25.8249]
distRefX = [7.4550, 7.4550, 7.4550, 7.4550]
distRefY = [8.6083, 8.6083, 8.6083, 8.6083]
numStates = 19
#And some constants
kBT = kB*T
beta = 1.0 / kBT
#First make sure all the input arrays have the same dimensions
numSims = len(simDirs)
allLens = np.array([len(a) for a in [kXY, refX, refY, distRefX, distRefY]])
#Want to loop over all trajectories provided, storing solute position information to calculate restraints
xyPos = None #X and Y coordinates of first heavy atom for all solutes - get shape later
nSamps = np.zeros((len(simDirs), numStates), dtype=int) #Have as many x-y restraints as sims and same number of lambda states for each
allPots = np.array([[]]*numStates).T #Potential energies, EXCLUDING RESTRAINT, for each simulation frame and lambda state
#Will also include pV term because may matter for configurations
xyBox = np.zeros(2)
for i, adir in enumerate(simDirs):
topFile = "%s/../sol_surf.top"%adir
trajFile = "%s/prod.nc"%adir
alchemicalFile = "%s/alchemical_output.txt"%adir
#First load in topology and get atom indices
top = pmd.load_file(topFile)
#Get solute heavy atoms for each solute
#Also get indices of surface atoms to use as references later
#Only taking last united atoms of first SAM molecule we find
heavyIndices = []
for res in top.residues:
if res.name not in ['OTM', 'CTM', 'STM', 'NTM', 'SOL']: #Assumes working with SAM surface...
thisheavyinds = []
for atom in res.atoms:
if not atom.name[0] == 'H':
thisheavyinds.append(atom.idx)
heavyIndices.append(thisheavyinds)
#Make into arrays for easier referencing
heavyIndices = np.array(heavyIndices)
#Load in the potential energies, INCLUDING RESTRAINT, at all states for this simulation to figure out frames to skip
alcDat = np.loadtxt(alchemicalFile)
startTime = alcDat[0, 1]
startFrame = int(startTime) - 1 #Be careful here... need write frequency in alchemical file to match exactly with positions
#AND assuming that have written in 1 ps increments...
#Also, first frame in trajectory is NOT at time zero, so subtract 1
thisPot = alcDat[:, 3:-1]
thispV = alcDat[:, -1]
#Next load in the trajectory and get all solute coordinates that matter
top.rb_torsions = pmd.TrackedList([])
top = pt.load_parmed(top, traj=False)
traj = pt.iterload(trajFile, top, frame_slice=(startFrame, -1))
nFrames = len(traj)
xyBox = np.array(traj[0].box.values)[:2] #A little lazy, but all boxes should be same and fixed in X and Y dimensions
thisxyPos = np.zeros((nFrames, len(heavyIndices), 2))
thisnSamps = np.zeros(numStates, dtype=int)
#Reference x and y coordinates for this restraint
thisRefXY = np.array([refX[i], refY[i]])
for j, frame in enumerate(traj):
thisPos = np.array(frame.xyz)
thisXY = thisPos[heavyIndices[:,0]][:, :2] #Takes XY coords for first heavy atom from each solute
thisxyPos[j,:] = thisXY
thisnSamps[int(alcDat[j, 2])] += 1 #Lambda states must be indexed starting at 0
#Also get wrapped positions relative to each reference face
#AND calculate xy restraint energy to remove by adding this for each solute
xyEnergy = 0.0
for k in range(len(heavyIndices)):
xy = thisXY[k]
#Then separately reimage around the restraint reference positions to calculate energy
xy = wl.reimage([xy], thisRefXY, xyBox)[0] - thisRefXY
xyEnergy += ( 0.5*kXY[i]*(0.5*(np.sign(xy[0] - distRefX[i]) + 1))*((xy[0] - distRefX[i])**2)
+ 0.5*kXY[i]*(0.5*(np.sign(xy[1] - distRefY[i]) + 1))*((xy[1] - distRefY[i])**2) )
#Remove the restraint energy (only for x-y restraint... z is the same in all simulations)
thisPot[j,:] -= (xyEnergy / kBT)
#And also add in pV contribution
thisPot[j,:] += thispV[j]
#Add to other things we're keeping track of
if xyPos is None:
xyPos = copy.deepcopy(thisxyPos)
else:
xyPos = np.vstack((xyPos, thisxyPos))
nSamps[i,:] = thisnSamps
allPots = np.vstack((allPots, thisPot))
#Now should have all the information we need
#Next, put it into the format that MBAR wants, adding energies as needed
Ukn = np.zeros((len(simDirs)*numStates, int(np.sum(nSamps))))
for i in range(len(simDirs)):
#First get energy of ith type of x-y restraint for all x-y positions
thisRefXY = np.array([refX[i], refY[i]])
#Must do by looping over each solute
xyEnergy = np.zeros(xyPos.shape[0])
for k in range(len(heavyIndices)):
xy = wl.reimage(xyPos[:,k,:], thisRefXY, xyBox) - thisRefXY
xyEnergy += ( 0.5*kXY[i]*(0.5*(np.sign(xy[:,0] - distRefX[i]) + 1))*((xy[:,0] - distRefX[i])**2)
+ 0.5*kXY[i]*(0.5*(np.sign(xy[:,1] - distRefY[i]) + 1))*((xy[:,1] - distRefY[i])**2) )
#Loop over alchemical states with this restraint and add energy
for j in range(numStates):
Ukn[i*numStates+j, :] = allPots[:,j] + (xyEnergy / kBT)
#Now should be set to run MBAR
mbarObj = mbar.MBAR(Ukn, nSamps.flatten())
#Following computePMF in MBAR to get configuration weights with desired potential of interest
logwCoupled = mbarObj._computeUnnormalizedLogWeights(allPots[:,0])
logwDecoupled = mbarObj._computeUnnormalizedLogWeights(allPots[:,-1])
#Also report average solute-system LJ and coulombic potential energies in the fully coupled ensemble
#(with restraints removed)
#Just printing these values
avgQ, stdQ = mbarObj.computeExpectations(allPots[:,0] - allPots[:,4], allPots[:,0])
avgLJ, stdLJ = mbarObj.computeExpectations(allPots[:,4] - allPots[:,-1], allPots[:,0])
print("\nAverage solute-system electrostatic potential energy: %f +/- %f"%(avgQ, stdQ))
print("Average solute-system LJ potential energy: %f +/- %f\n"%(avgLJ, stdLJ))
#Also print information that can be used to break free energy into components
#Start by just printing all of the free energies between states
alldGs, alldGerr = mbarObj.computePerturbedFreeEnergies(allPots.T)
print("\nAll free energies relative to first (coupled) state:")
print(alldGs.tolist())
print(alldGerr.tolist())
#And the free energy changes associated with just turning on LJ and elctrostatics separately
dGq = alldGs[0][0] - alldGs[0][4]
dGqErr = np.sqrt((alldGerr[0][0]**2) + (alldGerr[0][4])**2)
print("\nElectrostatic dG (with LJ on): %f +/- %f"%(dGq, dGqErr))
dGlj = alldGs[4][4] - alldGs[4][-1]
dGljErr = np.sqrt((alldGerr[4][4]**2) + (alldGerr[4][-1])**2)
print("\nLJ dG (no charges): %f +/- %f"%(dGlj, dGljErr))
#Now calculate average potential energy differences needed for computing relative entropies
dUq, dUqErr = mbarObj.computeExpectations(allPots[:,0] - allPots[:,4], allPots[:,0])
print("\nAverage electrostatic potential energy in fully coupled state: %f +/- %f"%(dUq, dUqErr))
dUlj, dUljErr = mbarObj.computeExpectations(allPots[:,4] - allPots[:,-1], allPots[:,4])
print("\nAverage LJ potential energy (no charges) in uncharged state: %f +/- %f"%(dUlj, dUljErr))
#And return weights after exponentiating log weights and normalizing
wCoupled = np.exp(logwCoupled)
wCoupled /= np.sum(wCoupled)
wDecoupled = np.exp(logwDecoupled)
wDecoupled /= np.sum(wDecoupled)
return wCoupled, wDecoupled
def main(args):
print time.ctime(time.time())
#Get topology file we're working with
topFile = args[0]
#And figure out if we're dealing with solute at surface or in bulk
if (args[1] == 'True'):
inBulk = True
else:
inBulk = False
if (args[2] == 'True'):
doReweight = True
else:
doReweight = False
#Read in topology file now to get information on solute atoms
top = pmd.load_file(topFile)
soluteInds = []
for res in top.residues:
if res.name not in ['OTM', 'CTM', 'STM', 'NTM', 'SOL']:
for atom in res.atoms:
soluteInds.append(atom.idx)
#Now define how we compute three-body angles with bins and cut-off
#Shell cut-off
shellCut = 3.32 #1st minimum distance for TIP4P-Ew water at 298.15 K and 1 bar
#Number of angle bins
nAngBins = 100 #500
#Define bin centers (should be nBins equally spaced between 0 and 180)
angBinCents = 0.5 * (np.arange(0.0, 180.001, 180.0/nAngBins)[:-1] + np.arange(0.0, 180.001, 180.0/nAngBins)[1:])
#And distance bins for local oxygen-oxygen RDF calculation
#(really distance histograms from central oxygens - can normalize however we want, really)
distBinWidth = 0.05
nDistBins = int(shellCut / distBinWidth)
distBins = np.arange(0.0, nDistBins*distBinWidth+0.00001, distBinWidth)
distBinCents = 0.5 * (distBins[:-1] + distBins[1:])
#Define the size of the probes used for assessing density fluctuations near solute
probeRadius = 3.3 # radius in Angstroms; the DIAMETER of a methane so assumes other atoms methane-sized
#And bins for numbers of waters in probes
probeBins = np.arange(0.0, 21.00001, 1.0)
nProbeBins = len(probeBins) - 1 #Will use np.histogram, which includes left edge in bin (so if want up to 20, go to 21)
#And will record number waters in each solvation shell (histograms of)
shellBins = np.arange(0.0, 251.00001, 1.0) #probably way too many bins, but don't want to run out
nShellBins = len(shellBins) - 1
#Should we do 2D histogram for angles and distances?
#Or also do 2D histogram for number of waters in probe and three-body angle?
#Interesting if make probe radius same size as three-body angle cutoff?
#Finally, also define the bins for computing RDFs of waters near all solute atoms
#Will use to define 1st and 2nd solvation shells
rdfBinWidth = 0.2
rdfMax = 12.00
rdfBins = np.arange(0.0, rdfMax+0.000001, rdfBinWidth)
rdfBinCents = 0.5 * (rdfBins[:-1] + rdfBins[1:])
nRDFBins = len(rdfBinCents)
rdfBinVols = (4.0*np.pi/3.0)*(rdfBins[1:]**3 - rdfBins[:-1]**3)
bulkDens = 0.0332 #Roughly right for TIP4P-EW at 298.15 K and 1 bar in inverse Angstroms cubed
#Need to create a variety of arrays to hold the data we're interested in
#Will record distributions in both 1st and 2nd solvation shells
shellCountsCoupled = np.zeros((nShellBins, 2)) #Histograms for numbers of waters in hydration shells of solutes
probeHistsCoupled = np.zeros((nProbeBins, 2)) #Histograms for numbers waters in probes in 1st and 2nd hydration shells
angHistsCoupled = np.zeros((nAngBins, 2)) #Histograms of three-body angles for water oxygens within solvation shells
distHistsCoupled = np.zeros((nDistBins, 2)) #Histograms of distances to water oxygens from central oxygens
solRDFsCoupled = np.zeros((nRDFBins, len(soluteInds))) #RDFs between each solute atom and water oxygens
shellCountsDecoupled = np.zeros((nShellBins, 2)) #Same as above, but decoupled state, not coupled state
probeHistsDecoupled = np.zeros((nProbeBins, 2))
angHistsDecoupled = np.zeros((nAngBins, 2))
distHistsDecoupled = np.zeros((nDistBins, 2))
solRDFsDecoupled = np.zeros((nRDFBins, len(soluteInds)))
#First need configuration weights to use in computing average quantities
#But only do if we're using a simuation with an expanded ensemble
if doReweight:
if inBulk:
weightsCoupled, weightsDecoupled = getConfigWeightsBulk(kB=1.0, T=1.0)
#Using 1 for kB and T because alchemical_output.txt should already have potential energies in kBT
simDirs = ['.']
else:
weightsCoupled, weightsDecoupled = getConfigWeightsSurf()
simDirs = ['Quad_0.25X_0.25Y', 'Quad_0.25X_0.75Y', 'Quad_0.75X_0.25Y', 'Quad_0.75X_0.75Y']
else:
weightsCoupled = np.array([])
weightsDecoupled = np.array([])
simDirs = ['.']
#To correctly match weights up to configurations, need to count frames from all trajectories
countFrames = 0
#Next, want to loop over all trajectories and compute RDFs from solute atoms to water oxygens
#Will use this to define solvation shells for finding other properties
#Actually, having looked at RDFs, just use 5.5 for first shell and 8.5 for second shell...
#AND use all atoms, including hydrogens, which have LJ interactions in GAFF2, to define shells
#Actually now only using heavy atoms... but when look at RDFs, examine all atoms
for adir in simDirs:
if doReweight:
#Before loading trajectory, figure out how many frames to exclude due to weight equilibration
alcDat = np.loadtxt(adir+'/alchemical_output.txt')
startTime = alcDat[0, 1]
startFrame = int(startTime) - 1
else:
startFrame = 0
top = pmd.load_file(topFile)
top.rb_torsions = pmd.TrackedList([]) #This is just for SAM systems so that it doesn't break pytraj
top = pt.load_parmed(top, traj=False)
traj = pt.iterload(adir+'/prod.nc', top, frame_slice=(startFrame, -1))
if not doReweight:
weightsCoupled = np.hstack((weightsCoupled, np.ones(len(traj))))
weightsDecoupled = np.hstack((weightsDecoupled, np.ones(len(traj))))
print("\nTopology and trajectory loaded from directory %s" % adir)
owInds = top.select('@OW')
soluteInds = top.select('!(:OTM,CTM,STM,NTM,SOL)')
print("\n\tFound %i water oxygens" % len(owInds))
print("\tFound %i solute atoms" % len(soluteInds))
for i, frame in enumerate(traj):
if i%1000 == 0:
print "On frame %i" % i
boxDims = np.array(frame.box.values[:3])
currCoords = np.array(frame.xyz)
#Wrap based on soluate atom center of geometry and get coordinates of interest
wrapCOM = np.average(currCoords[soluteInds], axis=0)
currCoords = wl.reimage(currCoords, wrapCOM, boxDims) - wrapCOM
owCoords = currCoords[owInds]
solCoords = currCoords[soluteInds]
#Loop over solute atoms and find pair-distance histograms with water oxygens
for j, acoord in enumerate(solCoords):
solRDFsCoupled[:,j] += (weightsCoupled[countFrames+i]
* wl.pairdistancehistogram(np.array([acoord]), owCoords, rdfBinWidth, nRDFBins, boxDims))
solRDFsDecoupled[:,j] += (weightsDecoupled[countFrames+i]
* wl.pairdistancehistogram(np.array([acoord]), owCoords, rdfBinWidth, nRDFBins, boxDims))
#Note that pairdistancehistogram is right-edge inclusive, NOT left-edge inclusive
#In practice, not a big difference
countFrames += len(traj)
#Finish by normalizing RDFs properly
for j in range(len(soluteInds)):
solRDFsCoupled[:,j] /= rdfBinVols #bulkDens*rdfBinVols
solRDFsDecoupled[:,j] /= rdfBinVols #bulkDens*rdfBinVols
if not doReweight:
solRDFsCoupled /= float(countFrames)
solRDFsDecoupled /= float(countFrames)
#And save to file
np.savetxt('solute-OW_RDFs_coupled.txt', np.hstack((np.array([rdfBinCents]).T, solRDFsCoupled)),
header='RDF bins (A) solute atom-OW RDF for solute atom indices %s'%(str(soluteInds)))
np.savetxt('solute-OW_RDFs_decoupled.txt', np.hstack((np.array([rdfBinCents]).T, solRDFsDecoupled)),
header='RDF bins (A) solute atom-OW RDF for solute atom indices %s'%(str(soluteInds)))
print("\tFound RDFs for water oxygens from solute indices.")
solShell1Cut = 5.5 #Angstroms from all solute atoms (including hydrogens)
solShell2Cut = 8.5
#And now that we know how many frames, we can assign real weights if not reweighting
if not doReweight:
weightsCoupled /= float(countFrames)
weightsDecoupled /= float(countFrames)
#Reset countFrames so get weights right
countFrames = 0
#Repeat looping over trajectories to calculate water properties in solute solvation shell
for adir in simDirs:
if doReweight:
#Before loading trajectory, figure out how many frames to exclude due to weight equilibration
alcDat = np.loadtxt(adir+'/alchemical_output.txt')
startTime = alcDat[0, 1]
startFrame = int(startTime) - 1
else:
startFrame = 0
top = pmd.load_file(topFile)
top.rb_torsions = pmd.TrackedList([]) #This is just for SAM systems so that it doesn't break pytraj
top = pt.load_parmed(top, traj=False)
traj = pt.iterload(adir+'/prod.nc', top, frame_slice=(startFrame, -1))
print("\nTopology and trajectory loaded from directory %s" % adir)
owInds = top.select('@OW')
soluteInds = top.select('!(:OTM,CTM,STM,NTM,SOL)&!(@H=)')
surfInds = top.select('(:OTM,CTM,STM,NTM)&!(@H=)') #For probe insertions, also include solute and surface heavy atoms
print("\n\tFound %i water oxygens" % len(owInds))
print("\tFound %i solute heavy atoms" % len(soluteInds))
print("\tFound %i non-hydrogen surface atoms" % len(surfInds))
if len(surfInds) == 0:
surfInds.dtype=int
for i, frame in enumerate(traj):
#if i%10 == 0:
# print "On frame %i" % i
boxDims = np.array(frame.box.values[:3])
currCoords = np.array(frame.xyz)
#Wrap based on soluate atom center of geometry and get coordinates of interest
wrapCOM = np.average(currCoords[soluteInds], axis=0)
currCoords = wl.reimage(currCoords, wrapCOM, boxDims) - wrapCOM
owCoords = currCoords[owInds]
solCoords = currCoords[soluteInds]
surfCoords = currCoords[surfInds]
#Now get solvent shells around solute
shell1BoolMat = wl.nearneighbors(solCoords, owCoords, boxDims, 0.0, solShell1Cut)
shell1Bool = np.array(np.sum(shell1BoolMat, axis=0), dtype=bool)
shell2BoolMat = wl.nearneighbors(solCoords, owCoords, boxDims, solShell1Cut, solShell2Cut)
shell2Bool = np.array(np.sum(shell2BoolMat, axis=0), dtype=bool)
#And add weight to histogram for numbers of waters in shells
thisCount1 = int(np.sum(shell1Bool))
shellCountsCoupled[thisCount1, 0] += weightsCoupled[countFrames+i]
shellCountsDecoupled[thisCount1, 0] += weightsDecoupled[countFrames+i]
thisCount2 = int(np.sum(shell2Bool))
shellCountsCoupled[thisCount2, 1] += weightsCoupled[countFrames+i]
shellCountsDecoupled[thisCount2, 1] += weightsDecoupled[countFrames+i]
#And compute water properties of solvent shells, first 3-body angles
thisAngs1, thisNumAngs1 = wp.getCosAngs(owCoords[shell1Bool], owCoords, boxDims, highCut=shellCut)
thisAngHist1, thisAngBins1 = np.histogram(thisAngs1, bins=nAngBins, range=[0.0, 180.0], density=False)
angHistsCoupled[:,0] += weightsCoupled[countFrames+i] * thisAngHist1
angHistsDecoupled[:,0] += weightsDecoupled[countFrames+i] * thisAngHist1
thisAngs2, thisNumAngs2 = wp.getCosAngs(owCoords[shell2Bool], owCoords, boxDims, highCut=shellCut)
thisAngHist2, thisAngBins2 = np.histogram(thisAngs2, bins=nAngBins, range=[0.0, 180.0], density=False)
angHistsCoupled[:,1] += weightsCoupled[countFrames+i] * thisAngHist2
angHistsDecoupled[:,1] += weightsDecoupled[countFrames+i] * thisAngHist2
#And ow-ow pair distance histograms in both shells as well
thisDistHist1 = wl.pairdistancehistogram(owCoords[shell1Bool], owCoords, distBinWidth, nDistBins, boxDims)
distHistsCoupled[:,0] += weightsCoupled[countFrames+i] * thisDistHist1
distHistsDecoupled[:,0] += weightsDecoupled[countFrames+i] * thisDistHist1
thisDistHist2 = wl.pairdistancehistogram(owCoords[shell2Bool], owCoords, distBinWidth, nDistBins, boxDims)
distHistsCoupled[:,1] += weightsCoupled[countFrames+i] * thisDistHist2
distHistsDecoupled[:,1] += weightsDecoupled[countFrames+i] * thisDistHist2
#Next compute distributions of numbers of waters in probes centered within each shell
#To do this, create random grid of points in SQUARE that encompasses both shells
#Then only keep points within each shell based on distance
#Square will be based on shell cutoffs and min and max coordinates in each dimension of solute
minSolX = np.min(solCoords[:,0]) - solShell2Cut
maxSolX = np.max(solCoords[:,0]) + solShell2Cut
minSolY = np.min(solCoords[:,1]) - solShell2Cut
maxSolY = np.max(solCoords[:,1]) + solShell2Cut
minSolZ = np.min(solCoords[:,2]) - solShell2Cut
maxSolZ = np.max(solCoords[:,2]) + solShell2Cut
thisGridX = minSolX + np.random.random(500)*(maxSolX - minSolX)
thisGridY = minSolY + np.random.random(500)*(maxSolY - minSolY)
thisGridZ = minSolZ + np.random.random(500)*(maxSolZ - minSolZ)
thisGrid = np.vstack((thisGridX, thisGridY, thisGridZ)).T
gridBoolMat1 = wl.nearneighbors(solCoords, thisGrid, boxDims, 0.0, solShell1Cut)
gridBool1 = np.array(np.sum(gridBoolMat1, axis=0), dtype=bool)
thisNum1 = wl.probegrid(np.vstack((owCoords, surfCoords, solCoords)), thisGrid[gridBool1], probeRadius, boxDims)
thisProbeHist1, thisProbeBins1 = np.histogram(thisNum1, bins=probeBins, density=False)
probeHistsCoupled[:,0] += weightsCoupled[countFrames+i] * thisProbeHist1
probeHistsDecoupled[:,0] += weightsDecoupled[countFrames+i] * thisProbeHist1
gridBoolMat2 = wl.nearneighbors(solCoords, thisGrid, boxDims, solShell1Cut, solShell2Cut)
gridBool2 = np.array(np.sum(gridBoolMat2, axis=0), dtype=bool)
thisNum2 = wl.probegrid(np.vstack((owCoords, surfCoords, solCoords)), thisGrid[gridBool2], probeRadius, boxDims)
thisProbeHist2, thisProbeBins2 = np.histogram(thisNum2, bins=probeBins, density=False)
probeHistsCoupled[:,1] += weightsCoupled[countFrames+i] * thisProbeHist2
probeHistsDecoupled[:,1] += weightsDecoupled[countFrames+i] * thisProbeHist2
countFrames += len(traj)
#Should have everything we need, so save to text files
np.savetxt('solute_shell_hists.txt',
np.hstack((np.array([shellBins[:-1]]).T, shellCountsCoupled, shellCountsDecoupled)),
header='Histograms of numbers of waters in first and second solute solvation shells with solvent in coupled (columns 2, 3) and decoupled (columns 4, 5) states')
np.savetxt('solute_probe_hists.txt',
np.hstack((np.array([probeBins[:-1]]).T, probeHistsCoupled, probeHistsDecoupled)),
header='Number waters in probe histograms in first and second solute solvation shells with solvent in coupled (columns 2, 3) and decoupled (columns 4, 5) states')
np.savetxt('solute_ang_hists.txt',
np.hstack((np.array([angBinCents]).T, angHistsCoupled, angHistsDecoupled)),
header='3-body angle histograms in first and second solute solvation shells with solvent in coupled (columns 2, 3) and decoupled (columns 4, 5) states')
np.savetxt('solute_pair_hists.txt',
np.hstack((np.array([distBinCents]).T, distHistsCoupled, distHistsDecoupled)),
header='O-O pair-distance histograms in first and second solute solvation shells with solvent in coupled (columns 2, 3) and decoupled (columns 4, 5) states')
print time.ctime(time.time())
def main(args):
print time.ctime(time.time())
#To define some things, read in the first simulation
#Will then assume all other simulations are set up in an identical way
#(i.e. same box size, same number of frames)
topFile = args[0]
simDirs = args[1:]
#First load in the topology and trajectory
top = pmd.load_file(topFile)
top.rb_torsions = pmd.TrackedList(
[]) #This is just for SAM systems so that it doesn't break pytraj
top = pt.load_parmed(top, traj=False)
traj = pt.iterload(simDirs[0] + '/prod.nc', top)
boxDims = np.array(traj[0].box.values[:3])
#Before starting, create bins in the x, y, and z-directions
#This will be used to define instantaneous interfaces and record some spatially varying interfacial properties
gridSize = 1.0 #Angstroms
xGrid = np.arange(-boxDims[0] / 2.0, boxDims[0] / 2.0 + gridSize,
gridSize) #Bins may overlap, but that's ok
yGrid = np.arange(-boxDims[1] / 2.0, boxDims[1] / 2.0 + gridSize, gridSize)
zGrid = np.arange((-boxDims[2] + boxDims[2] % gridSize) / 2.0,
(boxDims[2] - boxDims[2] % gridSize) / 2.0 + 0.001,
gridSize) #Symmetrizing grid in z direction
print "Using following coarse grids in x-, y-, and z-dimensions:"
print xGrid
print yGrid
print zGrid
#Define grid-point centers
xGridLocs = 0.5 * (xGrid[:-1] + xGrid[1:])
yGridLocs = 0.5 * (yGrid[:-1] + yGrid[1:])
zGridLocs = 0.5 * (zGrid[:-1] + zGrid[1:])
#And define grid sizes
xSize = len(xGridLocs)
ySize = len(yGridLocs)
zSize = len(zGridLocs)
#Now set-up fine grid for actually identifying the interface more precisely
zGridSize = 0.1 #Set separate grid size in z direction for a fine grid used for finding all density profiles
zGridFine = np.arange((-boxDims[2] + boxDims[2] % zGridSize) / 2.0,
(boxDims[2] - boxDims[2] % zGridSize) / 2.0 + 0.001,
zGridSize)
#Define grid-point centers for fine grid
zGridLocsFine = 0.5 * (zGridFine[:-1] + zGridFine[1:])
zSizeFine = len(zGridLocsFine)
#For calculating some properties as a function as distance from the surface, will use specific z slices
#While all the grid stuff is relative to surface SU atoms, want z slices relative to the interface itself
sliceGridSize = 0.5
zSlice = np.arange(-6.0, 12.000001, sliceGridSize)
zSliceLocs = 0.5 * (zSlice[:-1] + zSlice[1:])
zSliceSize = len(zSliceLocs)
#Set the default bulk density
bulkDens = 0.0332 #Roughly right for TIP4P-EW at 298.15 K and 1 bar in inverse Angstroms cubed
#Define the density fraction for determining the interface location
fracDens = 0.3 #this is lower than 0.5 which is usually used by Willard and others
#however, it puts the interface a little closer to the surface atoms and,
#as Willard says in his 2014 paper, any value between 0.3 and 0.7 works
densCut = fracDens * bulkDens
print "\nUsing bulk density value of %f (TIP4P-Ew at 1 bar and 298.15 K)." % bulkDens
print "To define interface, using a bulk density fraction of %f." % fracDens
#Define the size of the probes used for assessing hydrophobicity
probeRadius = 3.3 # radius in Angstroms; the DIAMETER of a methane (so assumes all other atoms methane-size)
#Now define how we compute three-body angles with bins and cut-off
#Shell cut-off
shellCut = 3.32 #1st minimum distance for TIP4P-Ew water at 298.15 K and 1 bar
#Number of angle bins
nAngBins = 100 #500
#Define bin centers (should be nBins equally spaced between 0 and 180)
angBinCents = 0.5 * (np.arange(0.0, 180.001, 180.0 / nAngBins)[:-1] +
np.arange(0.0, 180.001, 180.0 / nAngBins)[1:])
#And distance bins for local RDF calculation
#(really distance histograms from central oxygens - can normalize however we want, really)
distBinWidth = 0.05
nDistBins = int(shellCut / distBinWidth)
distBins = np.arange(0.0, nDistBins * distBinWidth + 0.00001, distBinWidth)
distBinCents = 0.5 * (distBins[:-1] + distBins[1:])
#And bins for numbers of waters in probes
probeBins = np.arange(0.0, 21.00001, 1.0)
nProbeBins = len(
probeBins
) - 1 #Will use np.histogram, which includes left edge in bin (so if want up to 20, go to 21)
#Should we do 2D histogram for angles and distances?
#Or also do 2D histogram for number of waters in probe and three-body angle?
#Interesting if make probe radius same size as three-body angle cutoff?
#Need to create a variety of arrays to hold the data we're interested in
interfaceZmean = np.zeros(
(xSize, ySize)
) #Average mean interface height at each x-y bin - same in all x-y bins
interfaceZ = np.zeros(
(xSize,
ySize)) #Average instantaneous interface height at each x-y bin
interfaceZSq = np.zeros(
(xSize, ySize
)) #Squared average interface height (to compute height fluctuations)
#This can be more easily compared to mean-field studies
watDensFine = np.zeros(
zSizeFine
) #Water density on finer grid for instantaneous interface definition
watDensFineMean = np.zeros(
zSizeFine) #Same but for mean interface definition
surfDensFine = np.zeros(
zSizeFine
) #Density profile for surface heavy atoms (ignores interface definition)
probeHists = np.zeros(
(nProbeBins, zSliceSize
)) #Histograms for numbers of waters in probes at each z-slice
angHists = np.zeros(
(nAngBins, zSliceSize)
) #Histograms of three-body angles for water oxygens within in each z-slice
distHists = np.zeros(
(nDistBins, zSliceSize
)) #Histograms of distances to water oxygens from central oxygens
probeHistsMean = np.zeros(
(nProbeBins,
zSliceSize)) #And same definitions but for mean interfaces
angHistsMean = np.zeros((nAngBins, zSliceSize))
distHistsMean = np.zeros((nDistBins, zSliceSize))
#Since will use multiple trajectories, also need to count total frames we're averaging over
totFrames = 0.0
#Now need to define variables to hold the surface points and normal vectors at each point
#Note that by surface points, here we just mean the INDICES of the x, y, and z grids
#To access the actual points, need to reference xGridLocs, etc.
#In the 'instant' interface definition, the exact locations of surface points changes, but
#only keep one surface point per x-y bin, so when project onto x-y plane to look at heat
#plots can use the same grid point locations as for the fixed, 'mean' interface
#With the 'mean' definition, this will be set below and unchanged when computing metrics
surfacePoints = np.zeros((xSize * ySize, 3), dtype=int)
surfaceNorms = np.zeros(
(xSize * ySize, 3)) #Should keep as normalized vectors throughout
surfacePointsMean = np.zeros((xSize * ySize, 3), dtype=int)
surfaceNormsMean = np.zeros((xSize * ySize, 3))
#But also want an actual list of all possible grid-point locations...
xmesh, ymesh, zmesh = np.meshgrid(np.arange(xSize), np.arange(ySize),
np.arange(zSize))
gridPoints = np.vstack(
(xmesh.flatten(), ymesh.flatten(), zmesh.flatten())).T
#At this point, want to actually loop over the simulation directories, load simulations,
#and do calculations for each frame
for adir in simDirs:
top = pmd.load_file(topFile)
top.rb_torsions = pmd.TrackedList(
[]) #This is just for SAM systems so that it doesn't break pytraj
top = pt.load_parmed(top, traj=False)
traj = pt.iterload(adir + '/prod.nc', top)
print("\nTopology and trajectory loaded from directory %s" % adir)
owInds = top.select('@OW')
surfInds = top.select('(:OTM,CTM,STM,NTM)&!(@H=)')
suInds = top.select('@SU')
print("\n\tFound %i water oxygens" % len(owInds))
print("\tFound %i non-hydrogen surface atoms" % len(surfInds))
print("\tFound %i SU surface atoms" % len(suInds))
nFrames = float(
traj.n_frames) #Make it a float to make averaging easier later
totFrames += nFrames
tempWatDensFineMean = np.zeros(zSizeFine)
#Find the mean interface definition to use for this trajectory
#Need to loop over the trajectory once and find mean interface location
for i, frame in enumerate(traj):
boxDims = np.array(frame.box.values[:3])
currCoords = np.array(frame.xyz)
#Need to do wrapping procedure by first putting surface together, then wrapping water around it
wrapCOM1 = currCoords[suInds[0]]
currCoords = wl.reimage(currCoords, wrapCOM1, boxDims) - wrapCOM1
wrapCOM2 = np.average(currCoords[suInds], axis=0)
currCoords = wl.reimage(currCoords, wrapCOM2, boxDims) - wrapCOM2
#Bin the current z coordinates
thisSurfDens, tempBins = np.histogram(currCoords[surfInds, 2],
bins=zGridFine,
normed=False)
thisWatDens, tempBins = np.histogram(currCoords[owInds, 2],
bins=zGridFine,
normed=False)
surfDensFine += thisSurfDens
tempWatDensFineMean += thisWatDens
#Record fine density, then normalize to number densities for next calculation
watDensFineMean += tempWatDensFineMean
tempWatDensFineMean = tempWatDensFineMean / (nFrames * boxDims[0] *
boxDims[1] * zGridSize)
#Find the average density in a region far from the surface to use as a reference
#Recall that the wrapping procedure puts the surface center of geometry at the origin
refOWdens = np.average(
0.5 * (tempWatDensFineMean[-int(1.0 / zGridSize) - 1:-1] +
tempWatDensFineMean[1:int(1.0 / zGridSize) + 1]))
#Above uses 1.0 A slices at edges of wrapped box
#It's a useful quantity to report, but better to just use fixed cut-off for all simulations...
print "\n\tDensity value in center of water phase (far from interface): %f" % refOWdens
#And find where the water density is half of its "bulk" value
#Exclude grid points near box edge because fluctuations in box lead to weird densities there
loInd = np.argmin(abs(tempWatDensFineMean[5:(zSizeFine / 2)] -
densCut))
print "\tOn lower surface, mean interface is at following Z-coordinate:"
print "\t Lower: %f" % zGridLocsFine[loInd]
#Now set up arrays of surface points and surface normal vectors - easy for mean interface
thisxmesh, thisymesh = np.meshgrid(np.arange(xSize, dtype=int),
np.arange(ySize, dtype=int))
surfacePointsMean[:, 0:2] = np.vstack(
(thisxmesh.flatten(), thisymesh.flatten())).T
surfacePointsMean[:, 2] = loInd
surfaceNormsMean[:,
2] = -1.0 #Just working with LOWER surface (solute is on top)
#Just go ahead and record the average interface height at each x and y bin, since it won't change
interfaceZmean[:, :] += zGridLocsFine[loInd]
#Now should be ready to loop over the trajectory using both interface definitions and computing things
print "\nPre-processing finished, starting main loop over trajectory."
for i, frame in enumerate(traj):
#if i%1000 == 0:
# print "On frame %i" % i
boxDims = np.array(frame.box.values[:3])
currCoords = np.array(frame.xyz)
#Need to do a wrapping procedure to more easily find waters within certain layers of surface
wrapCOM1 = currCoords[suInds[0]]
currCoords = wl.reimage(currCoords, wrapCOM1, boxDims) - wrapCOM1
wrapCOM2 = np.average(currCoords[suInds], axis=0)
currCoords = wl.reimage(currCoords, wrapCOM2, boxDims) - wrapCOM2
OWCoords = currCoords[owInds]
suCoords = currCoords[suInds]
surfCoords = currCoords[surfInds]
surfMidZ = np.average(suCoords[:, 2])
#Get actual locations of surface points (not just indices)
#Will overwrite with off-lattice x, y, and z positions for instantaneous interface
#Just use fine z-grid for mean definition
thisSurf = np.vstack(
(xGridLocs[surfacePoints[:, 0]], yGridLocs[surfacePoints[:,
1]],
zGridLocsFine[surfacePoints[:, 2]])).T
thisSurfMean = np.vstack((xGridLocs[surfacePointsMean[:, 0]],
yGridLocs[surfacePointsMean[:, 1]],
zGridLocsFine[surfacePointsMean[:,
2]])).T
#Use water coordinates to find instantaneous interface
#First need to find the density field
#Note that we use 2.4 as the smoothing length, as in Willard and Chandler, 2010
thisdensfield, thisdensnorms = wl.willarddensityfield(
OWCoords, xGridLocs, yGridLocs, zGridLocs, boxDims, 2.4)
#Next need to define the interface - using the marchinge cubes algorithm in scikit-image
verts, faces, normals, values = skmeasure.marching_cubes_lewiner(
thisdensfield, densCut, spacing=(gridSize, gridSize, gridSize))
#Shift the points returned...
verts[:, 0] += xGrid[0]
verts[:, 1] += yGrid[0]
verts[:, 2] += zGrid[0]
#And make sure the points are in the box
#Actually, for the purposes of making sure we have a single interface point for each x-y grid cell,
#we DO NOT want to wrap. This is because the grid may extend past the box size. For accurately
#calculating distances this is an issue because points outside the box will never overlap with
#wrapped atoms. But, we can't wrap now... have to wait until after we have our interface points.
#Below plot is for debugging only
#fig = plt.figure(figsize=(10, 10))
#ax = fig.add_subplot(111, projection='3d')
#ax.scatter(verts[:,0], verts[:,1], verts[:,2])
#ax.set_xlabel('X')
#ax.set_ylabel('Y')
#ax.set_zlabel('Z')
#fig.tight_layout()
#plt.show()
#Now need to trim the points so that we only have one point below the surface for
#each x-y bin. To do this, I'm taking the min z of the upper surface and max z of the lower surface.
#With this definition, hopefully odd blips in the bulk that satisfy the isosurface definition will be
#excluded.
newvertmat = np.ones(
(xSize, ySize,
3)) #Will flatten, but for now use data structure to help
newvertmat[:, :, 2] = -10000.0
#Loop over old vertices
for avert in verts:
thisXind = np.digitize([avert[0]], xGrid)[0] - 1
thisYind = np.digitize([avert[1]], yGrid)[0] - 1
#Check the lower interface
if (avert[2] < surfMidZ
and avert[2] > newvertmat[thisXind, thisYind, 2]
and avert[2] > zGrid[0]):
newvertmat[thisXind, thisYind, :] = avert
#Need to make sure that all x-y bins had a vertex in them...
#If not, use the z-value of one of the 4 adjacent points that isn't also too large
unfilledbins = np.where(abs(newvertmat[:, :, :]) == 10000.0)
for l in range(len(unfilledbins[0])):
ind1 = unfilledbins[0][l] #The x bin
ind2 = unfilledbins[1][l] #The y bin
newvertmat[ind1, ind2, 0] = xGridLocs[ind1]
newvertmat[ind1, ind2, 1] = yGridLocs[ind2]
#Use modulo operator to do wrapping
if abs(newvertmat[(ind1 - 1) % xSize, ind2, 2]) < 1000.0:
newvertmat[ind1, ind2, 2] = newvertmat[(ind1 - 1) % xSize,
ind2, 2]
elif abs(newvertmat[(ind1 + 1) % xSize, ind2, 2]) < 1000.0:
newvertmat[ind1, ind2, 2] = newvertmat[(ind1 + 1) % xSize,
ind2, 2]
elif abs(newvertmat[ind1, (ind2 - 1) % ySize, 2]) < 1000.0:
newvertmat[ind1, ind2,
2] = newvertmat[ind1, (ind2 - 1) % ySize, 2]
elif abs(newvertmat[ind1, (ind2 + 1) % ySize, 2]) < 1000.0:
newvertmat[ind1, ind2,
2] = newvertmat[ind1, (ind2 + 1) % ySize, 2]
#While the points are in a convenient format, record the interface height at each x-y bin
interfaceZ += newvertmat[:, :, 2]
interfaceZSq += newvertmat[:, :, 2]**2
#If the above procedure didn't fix the issue, just quit and recommend a finer z-grid size
unfilledbins = np.where(abs(newvertmat[:, :, 2]) == 10000.0)
if len(unfilledbins[0]) > 0:
print "Error: after trimming surface points, unable to find surface point for each x-y bin."
print "Could fix this by not using all bins and keeping track of bin counts, but maybe later."
print "Try and use a finer bin size in the z-dimension."
sys.exit(2)
#Now put together list of surface points (indices on pre-set grid) and exact locations (and unit normals)
newverts = np.reshape(newvertmat[:, :, :], (xSize * ySize, 3))
#fig = plt.figure(figsize=(10, 10))
#ax = fig.add_subplot(111, projection='3d')
#ax.scatter(newverts[:,0], newverts[:,1], newverts[:,2], c='gray')
#ax.set_xlabel('X')
#ax.set_ylabel('Y')
#ax.set_zlabel('Z')
#fig.tight_layout()
#plt.show()
surfacePoints[:, 0] = np.digitize(newverts[:, 0], xGrid) - 1
surfacePoints[:, 1] = np.digitize(newverts[:, 1], yGrid) - 1
surfacePoints[:, 2] = np.digitize(newverts[:, 2], zGrid) - 1
thisSurf = copy.deepcopy(newverts)
unusedDensVals, surfaceNorms = wl.willarddensitypoints(
OWCoords, thisSurf, boxDims, 2.4)
#print surfacePoints
#print thisSurf
#print surfaceNorms
#print np.linalg.norm(surfaceNorms, axis=1)
#At this point, MUST wrap our interface points into box so that distances from waters to them are accurate
#We couldn't do this earlier because we need to assign a single interface point to each x-y grid cell
thisSurf = wl.reimage(thisSurf, np.zeros(3), boxDims)
thisSurfMean = wl.reimage(thisSurfMean, np.zeros(3), boxDims)
#fig = plt.figure(figsize=(10, 10))
#ax = fig.add_subplot(111, projection='3d')
#ax.scatter(thisSurf[:,0], thisSurf[:,1], thisSurf[:,2], c='orange')
#ax.set_xlabel('X')
#ax.set_ylabel('Y')
#ax.set_zlabel('Z')
#fig.tight_layout()
#plt.show()
#Want to find the density profile
#To do this, first need to find which surface point closest to each water
#Then project that water's distance from the point along the surface normal
#This gives distances
#Note that surfaceNorms should be normalized to length 1!
#Also, don't worry about the random cutoff of 3.0 that I supplied... this is just part of the routine
#Really only want thisWatDists from this function - other stuff is not as useful for this code
thisWatClose, thisSurfClose, thisSliceNum, thisWatDists = wl.interfacewater(
OWCoords, thisSurf, surfaceNorms, 3.0, boxDims)
#Now add to the instantaneous fine water density profile - mean is already done
thisWatHist, tempBins = np.histogram(thisWatDists,
bins=zGridFine,
normed=False)
watDensFine += thisWatHist
#Now want to look at properties within z-slices moving normal to both interface definitions
#For three-body angles and pair distances, digitize waters for each interface definition
thisSliceInds = np.digitize(thisWatDists, zSlice) - 1
thisSliceIndsMean = np.digitize(
-1.0 *
(OWCoords[:, 2] - zGridLocsFine[surfacePointsMean[0, 2]]),
zSlice) - 1
#For probe insertions, placing probes at random x, y, and z locations within slices
#Make sure to wrap points after randomization to make sure not outside the simulation box
#Note different grid spacing for z slices, so need to do z separately
randomGrid = np.zeros(thisSurf.shape)
randomGrid[:, :2] = thisSurf[:, :2] + (np.random.random_sample(
(len(thisSurf), 2)) - 0.5) * 2.0 * gridSize
randomGrid[:, 2] = thisSurf[:, 2] + (np.random.random_sample(
len(thisSurf)) - 0.5) * 2.0 * sliceGridSize
randomGrid = wl.reimage(randomGrid, np.zeros(3), boxDims)
randomGridMean = np.zeros(thisSurfMean.shape)
randomGridMean[:, :2] = thisSurfMean[:, :2] + (
np.random.random_sample(
(len(thisSurfMean), 2)) - 0.5) * 2.0 * gridSize
randomGridMean[:,
2] = thisSurfMean[:, 2] + (np.random.random_sample(
len(thisSurfMean)) - 0.5) * 2.0 * sliceGridSize
randomGridMean = wl.reimage(randomGridMean, np.zeros(3), boxDims)
#And loop over z indices, selecting waters and calculating what we want in those slices
for j in range(zSliceSize):
thisSliceCoords = OWCoords[np.where(thisSliceInds == j)[0]]
thisSliceCoordsMean = OWCoords[np.where(
thisSliceIndsMean == j)[0]]
#Make sure we have waters in slices before attempting anything
if len(thisSliceCoords) > 0:
#Three-body angles
thisAngs, thisNumAngs = wp.getCosAngs(thisSliceCoords,
OWCoords,
boxDims,
highCut=shellCut)
thisAngHist, thisAngBins = np.histogram(thisAngs,
bins=nAngBins,
range=[0.0, 180.0],
density=False)
angHists[:, j] += thisAngHist
#Distance histograms with these slice oxygens as central oxygens
thisDistHist = wl.pairdistancehistogram(
thisSliceCoords, OWCoords, distBinWidth, nDistBins,
boxDims)
distHists[:, j] += thisDistHist
#Now probe occupancies
#Need to get random z locations within this slice
thisGrid = randomGrid + surfaceNorms * zSliceLocs[j]
thisNum = wl.probegrid(np.vstack((OWCoords, surfCoords)),
thisGrid, probeRadius, boxDims)
thisProbeHist, thisProbeBins = np.histogram(thisNum,
bins=probeBins,
density=False)
probeHists[:, j] += thisProbeHist
if len(thisSliceCoordsMean) > 0:
thisAngsMean, thisNumAngsMean = wp.getCosAngs(
thisSliceCoordsMean,
OWCoords,
boxDims,
highCut=shellCut)
thisAngHistMean, thisAngBinsMean = np.histogram(
thisAngsMean,
bins=nAngBins,
range=[0.0, 180.0],
density=False)
angHistsMean[:, j] += thisAngHistMean
thisDistHistMean = wl.pairdistancehistogram(
thisSliceCoordsMean, OWCoords, distBinWidth, nDistBins,
boxDims)
distHistsMean[:, j] += thisDistHistMean
thisGridMean = randomGridMean + surfaceNormsMean * zSliceLocs[j]
thisNumMean = wl.probegrid(np.vstack((OWCoords, surfCoords)),
thisGridMean, probeRadius, boxDims)
thisProbeHistMean, thisProbeBinsMean = np.histogram(
thisNumMean, bins=probeBins, density=False)
probeHistsMean[:, j] += thisProbeHistMean
#Done looping over trajectories, etc.
#Now finish computing some quantities by averaging appropriately
interfaceZmean /= float(len(simDirs))
interfaceZ /= totFrames
interfaceZSq /= totFrames
watDensFine /= (totFrames * boxDims[0] * boxDims[1] * zGridSize)
watDensFineMean /= (totFrames * boxDims[0] * boxDims[1] * zGridSize)
surfDensFine /= (totFrames * boxDims[0] * boxDims[1] * zGridSize)
#Just let the histograms be histograms... can normalize later if need to (don't think numbers will get too big)
#probeHists /= totFrames
#angHists /= totFrames
#distHists /= totFrames
#probeHistsMean /= totFrames
#angHistsMean /= totFrames
#distHistsMean /= totFrames
#Now save everything to files
#For 2D stuff (i.e. interfaces), use netCDF4 format
outdata = Dataset("interface_Z.nc", "w", format="NETCDF4", zlib=True)
#outdata.description("Interface heights (in the z-direction from surface atoms) and fluctuations for both mean and instantaneous interfaces.")
#outdata.history = "Created " + time.ctime(time.time())
xdim = outdata.createDimension("XGridPoints", xSize)
ydim = outdata.createDimension("YGridPoints", ySize)
outXLocs = outdata.createVariable("XGridPoints", "f8", ("XGridPoints", ))
outXLocs.units = "Angstroms"
outYLocs = outdata.createVariable("YGridPoints", "f8", ("YGridPoints", ))
outYLocs.units = "Angstroms"
outIntZ = outdata.createVariable("InterfaceHeightInstant", "f8", (
"XGridPoints",
"YGridPoints",
))
outIntZ.units = "Angstroms relative to SU surface atoms"
outIntZ[:, :] = interfaceZ
outIntZMean = outdata.createVariable("InterfaceHeightMean", "f8", (
"XGridPoints",
"YGridPoints",
))
outIntZMean.units = "Angstroms relative to SU surface atoms"
outIntZMean[:, :] = interfaceZmean
outIntZSq = outdata.createVariable("InterfaceHeightInstantSq", "f8", (
"XGridPoints",
"YGridPoints",
))
outIntZSq.units = "Squared Angstroms relative to SU surface atoms"
outIntZSq[:, :] = interfaceZSq
outdata.close()
#For everything else, just use text files, even though some may be a little big (i.e. angles and pair distances)
np.savetxt(
'z-densities.txt',
np.vstack(
(zGridLocsFine, surfDensFine, watDensFineMean, watDensFine)).T,
header=
'Distance normal to interface (A) Surface heavy atom density (1/A^3) Water oxygen density mean interface (at %f) Water oxygen density instantaneous interface'
% interfaceZmean[0, 0])
np.savetxt(
'probe_hists_mean.txt',
np.hstack((np.array([probeBins[:-1]]).T, probeHistsMean)),
header=
'Number waters in probe histograms at following distances from mean interface: %s'
% str(zSliceLocs))
np.savetxt(
'probe_hists_instant.txt',
np.hstack((np.array([probeBins[:-1]]).T, probeHists)),
header=
'Number waters in probe histograms at following distances from instantaneous interface: %s'
% str(zSliceLocs))
np.savetxt(
'ang3b_hists_mean.txt',
np.hstack((np.array([angBinCents]).T, angHistsMean)),
header=
'3-body angle histograms at following distances from mean interface: %s'
% str(zSliceLocs))
np.savetxt(
'ang3b_hists_instant.txt',
np.hstack((np.array([angBinCents]).T, angHists)),
header=
'3-body angle histograms at following distances from instantaneous interface: %s'
% str(zSliceLocs))
np.savetxt(
'pair_hists_mean.txt',
np.hstack((np.array([distBinCents]).T, distHistsMean)),
header=
'O-O pair-distance histograms at following distances from mean interface: %s'
% str(zSliceLocs))
np.savetxt(
'pair_hists_instant.txt',
np.hstack((np.array([distBinCents]).T, distHists)),
header=
'O-O pair-distance histograms at following distances from instantaneous interface: %s'
% str(zSliceLocs))
print time.ctime(time.time())
def main(args):
#Get the structure, topology, and trajectory files from the command line
#ParmEd accepts a wide range of file types (Amber, GROMACS, CHARMM, OpenMM... but not LAMMPS)
try:
topFile = args[0]
strucFile = args[1]
trajFile = args[2]
except IndexError:
print(
"Specify topology, structure, and trajectory files from the command line."
)
print(Usage)
sys.exit(2)
#And also allow user to specify start frame, but default to zero if no input
try:
startFrame = int(args[3])
except IndexError:
startFrame = 0
#And get information on whether or not to use a restraint
try:
boolstr = args[4]
if boolstr.lower() == 'true' or boolstr.lower() == 'yes':
restraintBool = True
else:
restraintBool = False
except IndexError:
restraintBool = False
print("Using topology file: %s" % topFile)
print("Using structure file: %s" % strucFile)
print("Using trajectory file: %s" % trajFile)
print("\nSetting up system...")
#Load in the files for initial simulations
top = pmd.load_file(topFile)
struc = pmd.load_file(strucFile)
#Transfer unit cell information to topology object
top.box = struc.box[:]
#Set up some global features to use in all simulations
temperature = 298.15 * u.kelvin
#Define the platform (i.e. hardware and drivers) to use for running the simulation
#This can be CUDA, OpenCL, CPU, or Reference
#CUDA is for NVIDIA GPUs
#OpenCL is for CPUs or GPUs, but must be used for old CPUs (not SSE4.1 compatible)
#CPU only allows single precision (CUDA and OpenCL allow single, mixed, or double)
#Reference is a clear, stable reference for other code development and is very slow, using double precision by default
platform = mm.Platform.getPlatformByName('CUDA')
prop = { #'Threads': '1', #number of threads for CPU - all definitions must be strings (I think)
'Precision':
'mixed', #for CUDA or OpenCL, select the precision (single, mixed, or double)
'DeviceIndex':
'0', #selects which GPUs to use - set this to zero if using CUDA_VISIBLE_DEVICES
'DeterministicForces':
'True' #Makes sure forces with CUDA and PME are deterministic
}
#Create the OpenMM system that can be used as a reference
systemRef = top.createSystem(
nonbondedMethod=app.
PME, #Uses PME for long-range electrostatics, simple cut-off for LJ
nonbondedCutoff=12.0 *
u.angstroms, #Defines cut-off for non-bonded interactions
rigidWater=True, #Use rigid water molecules
constraints=app.HBonds, #Constrains all bonds involving hydrogens
flexibleConstraints=
False, #Whether to include energies for constrained DOFs
removeCMMotion=
True, #Whether or not to remove COM motion (don't want to if part of system frozen)
)
#Set up the integrator to use as a reference
integratorRef = mm.LangevinIntegrator(
temperature, #Temperature for Langevin
1.0 / u.picoseconds, #Friction coefficient
2.0 * u.femtoseconds, #Integration timestep
)
integratorRef.setConstraintTolerance(1.0E-08)
#Get solute atoms and solute heavy atoms separately
soluteIndices = []
heavyIndices = []
for res in top.residues:
if res.name not in ['OTM', 'CTM', 'STM', 'NTM', 'SOL']:
for atom in res.atoms:
soluteIndices.append(atom.idx)
if 'H' not in atom.name[0]:
heavyIndices.append(atom.idx)
#If working with expanded ensemble simulation of solute near the interface, need to include restraint to keep close
if restraintBool:
#Also get surface SU atoms and surface CU atoms at top and bottom of surface
surfIndices = []
for atom in top.atoms:
if atom.type == 'SU':
surfIndices.append(atom.idx)
print("\nSolute indices: %s" % str(soluteIndices))
print("Solute heavy atom indices: %s" % str(heavyIndices))
print("Surface SU atom indices: %s" % str(surfIndices))
#Will now add a custom bonded force between heavy atoms of each solute and surface SU atoms
#Should be in units of kJ/mol*nm^2, but should check this
#Also, note that here we are using a flat-bottom restraint to keep close to surface
#AND to keep from penetrating into surface when it's in the decoupled state
refZlo = 1.4 * u.nanometer #in nm, the distance between the SU atoms and the solute centroid
refZhi = 1.7 * u.nanometer
restraintExpression = '0.5*k*step(refZlo - (z2 - z1))*(((z2 - z1) - refZlo)^2)'
restraintExpression += '+ 0.5*k*step((z2 - z1) - refZhi)*(((z2 - z1) - refZhi)^2)'
restraintForce = mm.CustomCentroidBondForce(2, restraintExpression)
restraintForce.addPerBondParameter('k')
restraintForce.addPerBondParameter('refZlo')
restraintForce.addPerBondParameter('refZhi')
restraintForce.addGroup(surfIndices, np.ones(
len(surfIndices))) #Don't weight with masses
#To assign flat-bottom restraint correctly, need to know if each solute is above or below interface
#Will need surface z-positions for this
suZpos = np.average(struc.coordinates[surfIndices, 2])
restraintForce.addGroup(heavyIndices, np.ones(len(heavyIndices)))
solZpos = np.average(struc.coordinates[heavyIndices, 2])
if (solZpos - suZpos) > 0:
restraintForce.addBond([0, 1], [10000.0, refZlo, refZhi])
else:
#A little confusing, but have to negate and switch for when z2-z1 is always going to be negative
restraintForce.addBond([0, 1], [10000.0, -refZhi, -refZlo])
systemRef.addForce(restraintForce)
#And define lambda states of interest
lambdaVec = np.array( #electrostatic lambda - 1.0 is fully interacting, 0.0 is non-interacting
[
[
1.00, 0.75, 0.50, 0.25, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00,
0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00
],
#LJ lambdas - 1.0 is fully interacting, 0.0 is non-interacting
[
1.00, 1.00, 1.00, 1.00, 1.00, 0.90, 0.80, 0.70, 0.60, 0.50,
0.40, 0.35, 0.30, 0.25, 0.20, 0.15, 0.10, 0.05, 0.00
]
])
#We need to add a custom non-bonded force for the solute being alchemically changed
#Will be helpful to have handle on non-bonded force handling LJ and coulombic interactions
NBForce = None
for frc in systemRef.getForces():
if (isinstance(frc, mm.NonbondedForce)):
NBForce = frc
#Turn off dispersion correction since have interface
NBForce.setUseDispersionCorrection(False)
#Separate out alchemical and regular particles using set objects
alchemicalParticles = set(soluteIndices)
chemicalParticles = set(range(
systemRef.getNumParticles())) - alchemicalParticles
#Define the soft-core function for turning on/off LJ interactions
#In energy expressions for CustomNonbondedForce, r is a special variable and refers to the distance between particles
#All other variables must be defined somewhere in the function.
#The exception are variables like sigma1 and sigma2.
#It is understood that a parameter will be added called 'sigma' and that the '1' and '2' are to specify the combining rule.
#Have also added parameter to switch the soft-core interaction to a WCA potential
softCoreFunctionWCA = '(step(x-0.5))*(4.0*lambdaLJ*epsilon*x*(x-1.0) + (1.0-lambdaWCA)*lambdaLJ*epsilon) '
softCoreFunctionWCA += '+ (1.0 - step(x-0.5))*lambdaWCA*(4.0*lambdaLJ*epsilon*x*(x-1.0));'
softCoreFunctionWCA += 'x = (1.0/reff_sterics);'
softCoreFunctionWCA += 'reff_sterics = (0.5*(1.0-lambdaLJ) + ((r/sigma)^6));'
softCoreFunctionWCA += 'sigma=0.5*(sigma1+sigma2); epsilon = sqrt(epsilon1*epsilon2)'
#Define the system force for this function and its parameters
SoftCoreForceWCA = mm.CustomNonbondedForce(softCoreFunctionWCA)
SoftCoreForceWCA.addGlobalParameter(
'lambdaLJ', 1.0
) #Throughout, should follow convention that lambdaLJ=1.0 is fully-interacting state
SoftCoreForceWCA.addGlobalParameter(
'lambdaWCA',
1.0) #When 1, attractions included; setting to 0 turns off attractions
SoftCoreForceWCA.addPerParticleParameter('sigma')
SoftCoreForceWCA.addPerParticleParameter('epsilon')
#Will turn off electrostatics completely in the original non-bonded force
#In the end-state, only want electrostatics inside the alchemical molecule
#To do this, just turn ON a custom force as we turn OFF electrostatics in the original force
ONE_4PI_EPS0 = 138.935456 #in kJ/mol nm/e^2
soluteCoulFunction = '(1.0-(lambdaQ^2))*ONE_4PI_EPS0*charge/r;'
soluteCoulFunction += 'ONE_4PI_EPS0 = %.16e;' % (ONE_4PI_EPS0)
soluteCoulFunction += 'charge = charge1*charge2'
SoluteCoulForce = mm.CustomNonbondedForce(soluteCoulFunction)
#Note this lambdaQ will be different than for soft core (it's also named differently, which is CRITICAL)
#This lambdaQ corresponds to the lambda that scales the charges to zero
#To turn on this custom force at the same rate, need to multiply by (1.0-lambdaQ**2), which we do
SoluteCoulForce.addGlobalParameter('lambdaQ', 1.0)
SoluteCoulForce.addPerParticleParameter('charge')
#Also create custom force for intramolecular alchemical LJ interactions
#Could include with electrostatics, but nice to break up
#We could also do this with a separate NonbondedForce object, but it would be a little more work, actually
soluteLJFunction = '4.0*epsilon*x*(x-1.0); x = (sigma/r)^6;'
soluteLJFunction += 'sigma=0.5*(sigma1+sigma2); epsilon=sqrt(epsilon1*epsilon2)'
SoluteLJForce = mm.CustomNonbondedForce(soluteLJFunction)
SoluteLJForce.addPerParticleParameter('sigma')
SoluteLJForce.addPerParticleParameter('epsilon')
#Loop over all particles and add to custom forces
#As we go, will also collect full charges on the solute particles
#AND we will set up the solute-solute interaction forces
alchemicalCharges = [[0]] * len(soluteIndices)
for ind in range(systemRef.getNumParticles()):
#Get current parameters in non-bonded force
[charge, sigma, epsilon] = NBForce.getParticleParameters(ind)
#Make sure that sigma is not set to zero! Fine for some ways of writing LJ energy, but NOT OK for soft-core!
if sigma / u.nanometer == 0.0:
newsigma = 0.3 * u.nanometer #This 0.3 is what's used by GROMACS as a default value for sc-sigma
else:
newsigma = sigma
#Add the particle to the soft-core force (do for ALL particles)
SoftCoreForceWCA.addParticle([newsigma, epsilon])
#Also add the particle to the solute only forces
SoluteCoulForce.addParticle([charge])
SoluteLJForce.addParticle([sigma, epsilon])
#If the particle is in the alchemical molecule, need to set it's LJ interactions to zero in original force
if ind in soluteIndices:
NBForce.setParticleParameters(ind, charge, sigma, epsilon * 0.0)
#And keep track of full charge so we can scale it right by lambda
alchemicalCharges[soluteIndices.index(ind)] = charge
#Now we need to handle exceptions carefully
for ind in range(NBForce.getNumExceptions()):
[p1, p2, excCharge, excSig,
excEps] = NBForce.getExceptionParameters(ind)
#For consistency, must add exclusions where we have exceptions for custom forces
SoftCoreForceWCA.addExclusion(p1, p2)
SoluteCoulForce.addExclusion(p1, p2)
SoluteLJForce.addExclusion(p1, p2)
#Only compute interactions between the alchemical and other particles for the soft-core force
SoftCoreForceWCA.addInteractionGroup(alchemicalParticles,
chemicalParticles)
#And only compute alchemical/alchemical interactions for other custom forces
SoluteCoulForce.addInteractionGroup(alchemicalParticles,
alchemicalParticles)
SoluteLJForce.addInteractionGroup(alchemicalParticles, alchemicalParticles)
#Set other soft-core parameters as needed
SoftCoreForceWCA.setCutoffDistance(12.0 * u.angstroms)
SoftCoreForceWCA.setNonbondedMethod(mm.CustomNonbondedForce.CutoffPeriodic)
SoftCoreForceWCA.setUseLongRangeCorrection(False)
systemRef.addForce(SoftCoreForceWCA)
#Set other parameters as needed - note that for the solute force would like to set no cutoff
#However, OpenMM won't allow a bunch of potentials with cutoffs then one without...
#So as long as the solute is smaller than the cut-off, won't have any problems!
SoluteCoulForce.setCutoffDistance(12.0 * u.angstroms)
SoluteCoulForce.setNonbondedMethod(mm.CustomNonbondedForce.CutoffPeriodic)
SoluteCoulForce.setUseLongRangeCorrection(False)
systemRef.addForce(SoluteCoulForce)
SoluteLJForce.setCutoffDistance(12.0 * u.angstroms)
SoluteLJForce.setNonbondedMethod(mm.CustomNonbondedForce.CutoffPeriodic)
SoluteLJForce.setUseLongRangeCorrection(False)
systemRef.addForce(SoluteLJForce)
#Need to add integrator and context in order to evaluate potential energies
#Integrator is arbitrary because won't use it
integrator = mm.VerletIntegrator(1.0 * u.femtoseconds)
context = mm.Context(systemRef, integrator, platform, prop)
##########################################################################
print("\nStarting analysis...")
kBT = u.AVOGADRO_CONSTANT_NA * u.BOLTZMANN_CONSTANT_kB * temperature
#Set up arrays to hold potential energies
#First row will be coupled, then no electrostatics, then no electrostatics with WCA, then decoupled
allU = np.array([[]] * 4).T
#We've now set everything up like we're going to run a simulation
#But now we will use pytraj to load a trajectory to get coordinates
#With those coordinates, we will evaluate the energies we want
#Just need to figure out if we have a surface or a bulk system
trajFiles = glob.glob('Quad*/%s' % trajFile)
if len(trajFiles) == 0:
trajFiles = [trajFile]
print("Using following trajectory files: %s" % str(trajFiles))
for aFile in trajFiles:
trajtop = copy.deepcopy(top)
trajtop.rb_torsions = pmd.TrackedList(
[]) #Necessary for SAM systems so doesn't break pytraj
trajtop = pt.load_parmed(trajtop, traj=False)
traj = pt.iterload(aFile, top=trajtop, frame_slice=(startFrame, -1))
thisAllU = np.zeros((len(traj), 4))
#Loop over the lambda states of interest, looping over whole trajectory each time
for i, lstate in enumerate([
[1.0, 1.0, 1.0], #Fully coupled
[1.0, 1.0, 0.0], #Charge turned off
[1.0, 0.0,
0.0], #Charged turned off, attractions turned off (so WCA)
[0.0, 1.0, 0.0]
]): #Decoupled (WCA still included, though doesn't matter)
#Set the lambda state
context.setParameter('lambdaLJ', lstate[0])
context.setParameter('lambdaWCA', lstate[1])
context.setParameter('lambdaQ', lstate[2])
for k, ind in enumerate(soluteIndices):
[charge, sig, eps] = NBForce.getParticleParameters(ind)
NBForce.setParticleParameters(ind,
alchemicalCharges[k] * lstate[2],
sig, eps)
NBForce.updateParametersInContext(context)
#And loop over trajectory
for t, frame in enumerate(traj):
thisbox = np.array(frame.box.values[:3])
context.setPeriodicBoxVectors(
np.array([thisbox[0], 0.0, 0.0]) * u.angstrom,
np.array([0.0, thisbox[1], 0.0]) * u.angstrom,
np.array([0.0, 0.0, thisbox[2]]) * u.angstrom)
thispos = np.array(frame.xyz) * u.angstrom
context.setPositions(thispos)
thisAllU[t, i] = context.getState(
getEnergy=True).getPotentialEnergy() / kBT
#Add this trajectory information
allU = np.vstack((allU, thisAllU))
#And that should be it, just need to save files and print information
#avgUq = np.average(allU[0,:] - allU[1,:])
#stdUq = np.std(allU[0,:] - allU[1,:], ddof=1)
#avgUlj = np.average(allU[1,:] - allU[2,:])
#stdUlj = np.std(allU[1,:] - allU[2,:], ddof=1)
#print("\nAverage solute-water electrostatic potential energy: %f +/- %f"%(avgUq, stdUq))
#print("Average solute-water LJ potential energy: %f +/- %f"%(avgUlj, stdUlj))
np.savetxt(
'pot_energy_decomp.txt',
allU,
header=
'U_coupled (kBT) U_noQ (kBT) U_noQ_WCA (kBT) U_decoupled (kBT) '
)
#Print some meaningful information
#Just make sure we do so as accurately as possible using alchemical information
alchFile = glob.glob('alchemical_U*.txt')[0]
print('Using alchemical information file: %s' % alchFile)
printInfo(allU, mbarFile='mbar_object.pkl', alchFile=alchFile)
def main(args):
#Get the structure and topology files from the command line
#ParmEd accepts a wide range of file types (Amber, GROMACS, CHARMM, OpenMM... but not LAMMPS)
try:
topFile = args[0]
strucFile = args[1]
except IndexError:
print("Specify topology and structure files from the command line.")
sys.exit(2)
print("Using topology file: %s" % topFile)
print("Using structure file: %s" % strucFile)
print("\nSetting up system...")
#Load in the files for initial simulations
top = pmd.load_file(topFile)
struc = pmd.load_file(strucFile)
#Transfer unit cell information to topology object
top.box = struc.box[:]
#Set up some global features to use in all simulations
temperature = 298.15 * u.kelvin
#Define the platform (i.e. hardware and drivers) to use for running the simulation
#This can be CUDA, OpenCL, CPU, or Reference
#CUDA is for NVIDIA GPUs
#OpenCL is for CPUs or GPUs, but must be used for old CPUs (not SSE4.1 compatible)
#CPU only allows single precision (CUDA and OpenCL allow single, mixed, or double)
#Reference is a clear, stable reference for other code development and is very slow, using double precision by default
platform = mm.Platform.getPlatformByName('CUDA')
prop = { #'Threads': '2', #number of threads for CPU - all definitions must be strings (I think)
'Precision':
'mixed', #for CUDA or OpenCL, select the precision (single, mixed, or double)
'DeviceIndex':
'0', #selects which GPUs to use - set this to zero if using CUDA_VISIBLE_DEVICES
'DeterministicForces':
'True' #Makes sure forces with CUDA and PME are deterministic
}
#Create the OpenMM system that can be used as a reference
systemRef = top.createSystem(
nonbondedMethod=app.
PME, #Uses PME for long-range electrostatics, simple cut-off for LJ
nonbondedCutoff=12.0 *
u.angstroms, #Defines cut-off for non-bonded interactions
rigidWater=True, #Use rigid water molecules
constraints=app.HBonds, #Constrains all bonds involving hydrogens
flexibleConstraints=
False, #Whether to include energies for constrained DOFs
removeCMMotion=
False, #Whether or not to remove COM motion (don't want to if part of system frozen)
)
#Set up the integrator to use as a reference
integratorRef = mm.LangevinIntegrator(
temperature, #Temperature for Langevin
1.0 / u.picoseconds, #Friction coefficient
2.0 * u.femtoseconds, #Integration timestep
)
integratorRef.setConstraintTolerance(1.0E-08)
#To freeze atoms, set mass to zero (does not apply to virtual sites, termed "extra particles" in OpenMM)
#Here assume (correctly, I think) that the topology indices for atoms correspond to those in the system
for i, atom in enumerate(top.atoms):
if atom.type in ('SU'): #, 'CU', 'CUO'):
systemRef.setParticleMass(i, 0 * u.dalton)
#Track non-bonded force, mainly to turn off dispersion correction
NBForce = None
for frc in systemRef.getForces():
if (isinstance(frc, mm.NonbondedForce)):
NBForce = frc
#Turn off dispersion correction since have interface
NBForce.setUseDispersionCorrection(False)
#Get solute atoms and solute heavy atoms separately
soluteIndices = []
heavyIndices = []
for res in top.residues:
if res.name not in ['OTM', 'CTM', 'STM', 'NTM', 'SOL']:
for atom in res.atoms:
soluteIndices.append(atom.idx)
if 'H' not in atom.name[0]:
heavyIndices.append(atom.idx)
#JUST for boric acid, add a custom bonded force
#Couldn't find a nice, compatible force field, but did find A forcefield, so using it
#But has no angle terms on O-B-O and instead a weird bond repulsion term
#This term also prevents out of plane bending
#Simple in our case because boric acid is symmetric, so only need one parameter
#Parameters come from Otkidach and Pletnev, 2001
#Here, Ad = (A^2) / (d^6) since Ai and Aj and di and dj are all the same
#In the original paper, B-OH bond had A = 1.72 and d = 0.354
#Note that d is dimensionless and A should have units of (Angstrom^3)*(kcal/mol)^(1/2)
#These units are inferred just to make things work out with kcal/mol and the given distance dependence
bondRepulsionFunction = 'Ad*(1.0/r)^6'
BondRepulsionForce = mm.CustomBondForce(bondRepulsionFunction)
BondRepulsionForce.addPerBondParameter(
'Ad') #Units are technically kJ/mol * nm^6
baOxInds = []
for aind in soluteIndices:
if top.atoms[aind].type == 'oh':
baOxInds.append(aind)
for i in range(len(baOxInds)):
for j in range(i + 1, len(baOxInds)):
BondRepulsionForce.addBond(baOxInds[i], baOxInds[j], [0.006289686])
systemRef.addForce(BondRepulsionForce)
#Also get surface SU atoms
surfIndices = []
for atom in top.atoms:
if atom.type == 'SU':
surfIndices.append(atom.idx)
startPos = np.array(struc.positions.value_in_unit(u.nanometer))
print("\nSolute indices: %s" % str(soluteIndices))
print("Solute heavy atom indices: %s" % str(heavyIndices))
print("Surface SU atom indices: %s" % str(surfIndices))
#Solute should already be placed far from the surface
#If this is not done right, or it is too close to half the periodic box distance, will have issues
#Either way, set this as the starting reference z distance
initRefZ = np.average(startPos[heavyIndices, 2]) - np.average(
startPos[surfIndices, 2])
print(initRefZ)
#Will now add a custom bonded force between solute heavy atoms and surface SU atoms
#Should be in units of kJ/mol*nm^2, but should check this
#For expanded ensemble, fine to assume solute is less than half the box distance from the surface
#But for umbrella sampling, want to apply pulling towards surface regardless of whether pull from above or below
#Also allows us to get further from the surface with our umbrellas without worrying about PBCs
restraintExpression = '0.5*k*(abs(z2 - z1) - refZ)^2'
restraintForce = mm.CustomCentroidBondForce(2, restraintExpression)
restraintForce.addPerBondParameter('k')
restraintForce.addGlobalParameter(
'refZ', initRefZ) #Make global so can modify during simulation
restraintForce.addGroup(surfIndices, np.ones(
len(surfIndices))) #Don't weight with masses
restraintForce.addGroup(heavyIndices, np.ones(len(heavyIndices)))
restraintForce.addBond([0, 1], [1000.0])
restraintForce.setUsesPeriodicBoundaryConditions(
True) #Only when doing umbrella sampling
systemRef.addForce(restraintForce)
forceLabelsRef = getForceLabels(systemRef)
decompEnergy(systemRef,
struc.positions,
labels=forceLabelsRef,
verbose=False)
#Do NVT simulation
stateFileNVT1, stateNVT1 = doSimNVT(top,
systemRef,
integratorRef,
platform,
prop,
temperature,
pos=struc.positions)
#Do pulling simulation - really I'm just slowly changing the equilibrium bond distance between the surface and the solute
stateFilePull, statePull = doSimPull(top,
systemRef,
integratorRef,
platform,
prop,
temperature,
state=stateFileNVT1)
decompEnergy(systemRef, statePull, labels=forceLabelsRef, verbose=False)
#Load in pulling restraint data and pulling trajectory to identify starting structures for each umbrella
pullData = np.loadtxt('pull_restraint.txt')
trajtop = copy.deepcopy(top)
trajtop.rb_torsions = pmd.TrackedList([])
trajtop = pt.load_parmed(trajtop, traj=False)
pulltraj = pt.iterload('pull.nc', trajtop)
frameTimes = np.array([frame.time for frame in pulltraj])
#Define some umbrella distances based on a fixed spacing between initial and final pulling coordinate
#Actually for final pulling coordinate, close to the surface, using average of actual coordinate and reference
zSpace = 0.1 #nm
zUmbs = np.arange(0.5 * (pullData[-1, 1] + pullData[-1, 2]),
pullData[0, 2], zSpace)
print("\nUsing following umbrellas:")
print(zUmbs)
#Then loop over umbrellas and run simulation for each
for i, zRefDist in enumerate(zUmbs):
os.mkdir("umbrella%i" % i)
os.chdir("umbrella%i" % i)
#Find where in the pulling trajectory the solute came closest to this umbrella
pullDatInd = np.argmin(abs(pullData[:, 2] - zRefDist))
frameInd = np.argmin(abs(frameTimes - pullData[pullDatInd, 0]))
#Get starting coordinates
#Making sure to assign the units that will be returned by pytraj
thisCoords = np.array(pulltraj[frameInd].xyz) * u.angstrom
#Set reference value for harmonic force
restraintForce.setGlobalParameterDefaultValue(0, zRefDist)
print("\nUmbrella %i:" % i)
print("\tReference distance: %f" % zRefDist)
print("\tFrame chosen from trajectory: %i (%f ps)" %
(frameInd, frameTimes[frameInd]))
#And run simulations, first equilibrating in NVT, then NPT, then production in NPT
stateFileNVT, stateNVT = doSimNVT(top,
systemRef,
integratorRef,
platform,
prop,
temperature,
pos=thisCoords)
stateFileNPT, stateNPT = doSimNPT(top,
systemRef,
integratorRef,
platform,
prop,
temperature,
state=stateFileNVT)
stateFileProd, stateProd = doSimUmbrella(top,
systemRef,
integratorRef,
platform,
prop,
temperature,
state=stateFileNPT)
os.chdir("../")
def main(args):
print('\nReading in files and obtaining LJ information...')
#First read in topology and trajectory
topFile = args[0]
trajFile = args[1]
top = pmd.load_file(topFile)
trajtop = copy.deepcopy(top)
trajtop.rb_torsions = pmd.TrackedList(
[]) #Necessary for SAM systems so doesn't break pytraj
trajtop = pt.load_parmed(trajtop, traj=False)
traj = pt.iterload(trajFile, top=trajtop)
#Next use parmed to get LJ parameters for all atoms in the solute, as well as water oxygens and surface atoms
#While go, also collect dictionaries of atomic indices associated with each atom type
#Will have to check separately when looking at overlaps with solute
soluteLJ = []
soluteInds = []
dictOtherLJ = {}
dictOtherInds = {}
for res in top.residues:
if res.name not in ['OTM', 'CTM', 'STM', 'NTM', 'SOL']:
for atom in res.atoms:
soluteInds.append(atom.idx)
soluteLJ.append([atom.sigma, atom.epsilon])
else:
for atom in res.atoms:
if not atom.type in dictOtherInds:
dictOtherInds[atom.type] = [atom.idx]
else:
dictOtherInds[atom.type].append(atom.idx)
if not atom.type in dictOtherLJ:
dictOtherLJ[atom.type] = np.array(
[atom.sigma, atom.epsilon])
soluteLJ = np.array(soluteLJ)
print(soluteLJ)
#Use Lorentz-Berthelot combining rules to get LJ parameters between each solute atom and a water oxygen
dictMixLJ = {}
for i in range(soluteLJ.shape[0]):
for akey in dictOtherLJ:
dictMixLJ['%i_%s' % (i, akey)] = np.array([
0.5 * (soluteLJ[i, 0] + dictOtherLJ[akey][0]),
np.sqrt(soluteLJ[i, 1] * dictOtherLJ[akey][1])
])
for key, val in dictMixLJ.iteritems():
print("%s, %s" % (key, str(val.tolist())))
print(
'\nDetermining hard-sphere radii for all combinations of solute and other system atoms...'
)
#Next compute hard-sphere radii by integrating according to Barker and Hendersen, Weeks, etc.
#In order to this right, technically using WCA potential, not LJ
hsRadii = {}
rvals = np.arange(0.0, 50.005, 0.005)
betaLJ = 1.0 / ((1.9872036E-03) * 298.15)
for i in range(soluteLJ.shape[0]):
for akey in dictOtherLJ:
[thisSig, thisEps] = dictMixLJ['%i_%s' % (i, akey)]
if thisEps == 0.0:
hsRadii['%i_%s' % (i, akey)] = 0.0
continue
thisRmin = thisSig * (2.0**(1.0 / 6.0))
thisSigdRmin6 = (thisSig / thisRmin)**6
thisPotRmin = 4.0 * thisEps * ((thisSigdRmin6**2) - thisSigdRmin6)
thisSigdR6 = (thisSig / rvals)**6
thisPotVals = 4.0 * thisEps * (
(thisSigdR6**2) - thisSigdR6) - thisPotRmin
thisPotVals[np.where(rvals >= thisRmin)] = 0.0
thisPotVals *= betaLJ
thisIntegrand = 1.0 - np.exp(-thisPotVals)
thisIntegrand[0] = 1.0
hsRadii['%i_%s' % (i, akey)] = simps(thisIntegrand, rvals)
#Need to multiply by two because will use atom centers to check overlap? Is Rhs distance between centers?
for key, val in hsRadii.iteritems():
print("%s, %f" % (key, val))
#Keep track of hard-sphere radii with water oxygens specially
solOWhsRadii = np.zeros(soluteLJ.shape[0])
for i in range(soluteLJ.shape[0]):
solOWhsRadii[i] = hsRadii['%i_OW_tip4pew' %
i] #Only using TIP4P/EW here
print('\nStarting loop over trajectory...')
#Now loop over trajectory and check if solute is overlapping with any waters OR surface atoms
#Will create a distribution of overlapping atoms
numOverlap = np.arange(101.0)
countOverlap = np.zeros(len(numOverlap))
#And also track average solute volume that we're trying to insert
solVol = 0.0
countFrames = 0
print('')
for frame in traj:
if countFrames % 100 == 0:
print("On frame %i" % countFrames)
countFrames += 1
boxDims = np.array(frame.box.values[:3])
currCoords = np.array(frame.xyz)
#Get solute coordinates and make sure solute is whole
#Then get solute coordinates relative to first solute atom
#Don't need any other wrapping because wl.nearneighbors will do its own wrapping
solCoords = currCoords[soluteInds]
solRefCoords = wl.reimage(solCoords, solCoords[0],
boxDims) - solCoords[0]
#While we have the coordinates nice, compute solute volume
#Do this based on hard-sphere radii to water oxygens, which is the most likely case anyway
solVol += np.sum(wl.spherevolumes(solRefCoords, solOWhsRadii, 0.1))
#Will shift the solute first atom (and others too) to a number of random locations
#Since applying restraint (if have surface) Z is drawn from the distribution we want
#X and Y can be drawn more easily from uniform distributions, so do this to randomize solute position
numRandXY = 1000
randX = np.random.random(numRandXY) * boxDims[0]
randY = np.random.random(numRandXY) * boxDims[1]
#And will keep track of number of overlapping atoms for each solute random position
thisTotOverlap = np.zeros(numRandXY, dtype=int)
#Loop over all non-solute atoms in the system by atom type
for akey, val in dictOtherInds.iteritems():
#For this specific atom type, need to keep track of WHICH neighbors overlapping
#And need to do for EACH solute atom
#Don't want to double-count if two solute atoms both overlap the same other atom
overlapBool = np.zeros((numRandXY, len(val)), dtype=int)
#Now loop over each solute atom
for i, coord in enumerate(solRefCoords):
thisRadius = hsRadii['%i_%s' % (i, akey)]
if thisRadius == 0.0:
continue
#Define coordinates of the current solute atom we're working with
#So setting first atom to random XY position, then shifting by distance to first atom
hsCoords = np.zeros((numRandXY, 3))
hsCoords[:, 0] = coord[0] + randX
hsCoords[:, 1] = coord[1] + randY
hsCoords[:, 2] = coord[2] + solCoords[0, 2]
#Identify boolean for overlapping atoms and add to overall boolean for overlap
#Note that want OR operation, so adding boolean arrays
overlapBool += wl.nearneighbors(hsCoords, currCoords[val],
boxDims, 0.0, thisRadius)
#For this non-solute atom type, add number of atoms overlapping with ANY solute atom
thisTotOverlap += np.sum(np.array(overlapBool, dtype=bool), axis=1)
thisBins = np.arange(np.max(thisTotOverlap) + 1)
countOverlap[thisBins] += np.bincount(thisTotOverlap)
print(countOverlap.tolist())
print('Hard-sphere solute insertion probability: %f' %
(-np.log(countOverlap[0] / np.sum(countOverlap))))
#Save the distribution to file
np.savetxt(
'HS-solute_overlap_hist.txt',
np.vstack((numOverlap, countOverlap)).T,
header=
'Number of non-solute atoms overlapping Histogram count')
solVol /= float(len(traj))
print(
'Average solute hard-sphere volume (based on water oxygen LJ params): %f'
% (solVol))
def static_DAT_restraint(
restraint_mask_list,
num_window_list,
ref_structure,
force_constant,
continuous_apr=True,
amber_index=False,
):
""" Create a static restraint """
# Setup reference structure
if isinstance(ref_structure, str):
ref_structure = utils.return_parmed_structure(ref_structure)
elif isinstance(ref_structure, pmd.structure.Structure):
pass
else:
raise Exception(
"static_DAT_restraint does not support the type associated with ref_structure:"
+ type(ref_structure))
ref_traj = pt.load_parmed(ref_structure, traj=True)
# Check num_window_list
if len(num_window_list) != 3:
raise Exception(
"The num_window_list needs to contain three integers corresponding to the number of windows in the attach, pull, and release phase, respectively"
)
# Setup restraint
rest = DAT_restraint()
rest.continuous_apr = continuous_apr
rest.amber_index = amber_index
rest.topology = ref_structure
rest.mask1 = restraint_mask_list[0]
rest.mask2 = restraint_mask_list[1]
if len(restraint_mask_list) >= 3:
rest.mask3 = restraint_mask_list[2]
if len(restraint_mask_list) == 4:
rest.mask4 = restraint_mask_list[3]
# Target value
mask_string = " ".join(restraint_mask_list)
if len(restraint_mask_list) == 2:
# Distance restraint
target = pt.distance(ref_traj, mask_string)[0]
elif len(restraint_mask_list) == 3:
# Angle restraint
target = pt.angle(ref_traj, mask_string)[0]
elif len(restraint_mask_list) == 4:
# Dihedral restraint
target = pt.dihedral(ref_traj, mask_string)[0]
else:
raise Exception(
"The number of masks (" + str(len(restraint_mask_list)) +
") in restraint_mask_list is not 2, 3, or 4 and thus is not one of the supported types: distance, angle, dihedral"
)
# Attach phase
if num_window_list[0] is not None and num_window_list[0] != 0:
rest.attach["target"] = target
rest.attach["fc_initial"] = force_constant
rest.attach["fc_final"] = force_constant
rest.attach["num_windows"] = num_window_list[0]
# Pull phase
if num_window_list[1] is not None and num_window_list[1] != 0:
rest.pull["fc"] = force_constant
rest.pull["target_initial"] = target
rest.pull["target_final"] = target
rest.pull["num_windows"] = num_window_list[1]
# Release phase
if num_window_list[2] is not None and num_window_list[2] != 0:
rest.release["target"] = target
rest.release["fc_initial"] = force_constant
rest.release["fc_final"] = force_constant
rest.release["num_windows"] = num_window_list[2]
rest.initialize()
return rest