Overview:

In the top (./), ./generate, ./analysis, ./analysis/asciiMod, ./analysis/xyzMod, and ./analysis/functions directories, you can make the executables in the directory with:

	make

Install to ~/bin/ with:

	make install

And clean the directory with:

	make clean

Running, for example, a vesicle simulation can be performed by:

	liposome testLipo $RANDOM 80000 3.45
	MD testLipo

Running on a slurm cluster can be performed by creating a submission script, such as submit.sh in this project, and running:

	cp submit.sh test/
	cd test
	sbatch submit.sh

Alternatively, if you make MD.cpp, or any other executable, on its own:

	g++ -O3 -fopenmp MD.cpp -o MD
	mkdir ~/bin/
	cp MD ~/bin/

Compiling MDcuda.cu on University of Memphis cluster (this one only implements tension, bonding, bending, and non-bonded interactions):

	module load cuda11.2/toolkit
	make cuda

The MDcuda executable can be used in place of the MD executable (with no other modifications).

Top (./) directory:

./MD.cpp:

The simulation solver. Runs with openmp or single threaded. Makefile contains build options for the intel (icc) compiler version. Using this is easy if you generate an mpd file in a directory (like test):

	make
	make install
	cd generate
	make liposome
	cp liposome ~/bin
	cd ../test
	liposome testLipo $(RANDOM) 5000 3.45
	MD testLipo

./generate directory:

Generates a variety of configurations (.mpd files). Executables include:

• bendComposition: Creates a flat bilayer with variable lipid length and 2 lipid types.
• bilayer: Creates a flat bilayer.
• build: Creates a flat bilayer.
• continuumSphereAndBilayer: Creates a flat bilayer with a point like nanoparticle.
• continuumSphereAndLiposome: Creates a spherical bilayer with a point like nanoparticle.
• continuumSphereAndLiposomeWrapped: Creates a fully liposome wrapped point like nanoparticle.
• continuumSphereGrid: Creates a flat bilayer with a lattice of point like nanoparticles.
• continuumSphereSurfactant: Creates a flat bilayer with surfactant particles that adhear to a point like nanoparticle and bilayer.
• domain: Creates a flat bilayer with 2 lipid types in a domain.
• gas: Creates a gas of particles.
• lipoCyto: Creates a spherical bilayer with a cytoskeleton.
• liposome: Creates a spherical bilayer.
• nanoSphereAndBilayer: Creates a solid nanoparticle and a flat bilayer.
• nanoSphereGrid: Creates a grid of solid nanoparticles and a flat bilayer.
• nanoSphereModBilayer:
• rigidNano: Creates a solid nanoparticle.
• scl: simple cubic lattice. Mostly for example.
• setMDConstants: Set molecular dynamics constants. Mostly for example.
• setMDConstants_UminAH: Set molecular dynamics constants. Mostly for example.
• solventBilayer: Creates a flat bilayer with solvent.
• solvent: Creates a gas of solvent.
• tetrahedron: Creates a tetrahedron. Mostly for example.
• tube: Creates a tubular bilayer.

./analysis directory:

Do analysis and modifications of systems (with .mpd files). Executables include:

• addBond: Add a bond to a system.
• adjustConstants: Adjust constants of a system.
• adjustMolecule: Adjust a moleucle of a system.
• boundaryPotential: Add a boundary potential to a system.
• chainBend: Calculates bending angle of lipids.
• chainBendLeaflet: Calculates bending angle of lipids per leaflet.
• changeDeltaT: Adjust timestep accuracy.
• changeFrame: Modify current system's frame.
• changeSeed: Modify the system's seed.
• changeTemperature: Modify the system's temperature.
• changeTension: Modify the system's tension.
• changeTime: Modify the system's start and end times.
• cluster: Calculates cluster sizes.
• clusterDomains: Calculates number of cluster domains.
• curvature3D_v7: Calculates curvature energy of a bilayer system.
• cycleXYZ: Cycle through a system's xyz file. Mostly for example.
• cylinderFluctuation: Calculates cylinder fluctuations?
• diffusion: Calculates diffusion. Make sure system store step is short enough to prevent jumps.
• duplicateImage: Duplicates a system across a dimension.
• extractXYZ: Extract the current XYZ position's of a system.
• forceBeadBead: Generates a graph of point like nanoparticles to other point like nanoparticles.
• forceBead: Generates a graph of point like nanoparticles to normal particles.
• frameReadPerSecond: Cycle through XYZ file. Mostly for example. Includes a timer.
• framesBeadParticleCount: Counts how many beads of a particular type there are in a system.
• frames: Cycle frames? Mostly example.
• framesDensity: Calculates density of a frame.
• framesDistanceBetweenIndices: Distances between two particle indices by frame.
• framesFlipFlop: Calculates lipid flip flop through by frame.
• framesPotentialTypePairs: Calculates potential between two types of particles.
• framesPotentialTypePairsList: Calculates potential between two types of particles and dumps a list of those.
• heightMap: Generates a height map from a flat system along z direction.
• heightMapFrames: Generates a height map from a flat system along z direction for every frame.
• lsPotentials: Dumps the non-bonded potential matricies of a system.
• lsProjection: Dumps a graphical projection of a system along 3 primary axii.
• modBond: Modify the a particular bonding interaction.
• modContinuumSphere: Modify a particular point like nanoparticle interaction.
• modContinuumSphereLong: Modify a particular point like nanoparticle interaction along with range (r_c).
• modSize: Modify a system's size.
• momentOfInertia: Calculation the moment of inertia of a system by frame.
• momentOfInertiaXYZ: Generate the axii for the moment of inertia of a system by frame.
• MSD: Mean square displacement. Diffusion.
• nanoPotential: Nanoparticle potential of a solid nanoparticle.
• nanoVsCOM: Nanoparticle center of mass distances by frame.
• neckBleb: Calculates the size of a neck near a bleb.
• netVel: Calculates the net velocity of a system.
• NPAngleFrames: Calculates the angle between point like nanoparticles and center of mass of a liposomes.
• nShapes: Counts the number of blebs in a system. Could be used to count exclusions from some particle.
• particleDistances: Distances between two particles in a system.
• potentialBeadBead: Makes a graph of potential between two point like nanoparticles.
• potentialBead: Makes a graph of potential between a point like nanoparticle and another particle.
• potential: Makes a graph of potential between particles.
• profile: Slices a system along one of the three primary axii.
• projectedCurvature: Projected curvature per layer. Use curvature_v7 instead.
• radial: Radial profile of other particles near a given particle.
• recenterFrames: Recenter the frames around a type, index, or molecule.
• removeSolvent: Remove solvent from a system's XYZ file.
• rollProfile: Obtains the center of mass and rolling angle of a solid nanoparticle.
• rotateXYZ: Rotate an xyz file along an axis.
• rProfile: Radial profile density around a cluster of particles in a system.
• rProfileFrames: Radial profile density around a cluster of particles in a system's XYZ file.
• singlePotential: Non-bonded potential of a single particle.
• singlePotentialType: Non-bonded potential of a single particle type.
• singlePotentialTypeHist: Histogram of a non-bonded potential of a single particle type.
• singlePotentialTypePairs: Non-bonded potential between two particle types.
• spherocity: Calculates the root mean square of a liposome.
• structureFactor: Calculates the structure factor of a flat bilayer.
• structureFactorFrames: Calculates the structure factor of a flat bilayer by frame.
• surface: Counts the number of surfaces in a system of types seperated by some cutoff.
• threeBodyDistribution: Average angular distribution of molecules.
• trajectoryFrame: Dumps trajectories by frame. Uses frames_name.xyz.
• translate: Move a system by some offset.
• twoBodyDistribution: Average distance distribution of molecules.
• typeDistribution: Calculates radial histogram of certain types along surfaces.
• vesicleRadius: Calculates radius of vesicle by frame.
• zPotential: Non-bonded potential histogram along z direction.
• zPotentialFrames: Non-bonded potential histograms along z direction for frames.
• zProfile: Histogram of particle probabilities. Bilayer profile.

./analysis/asciiMod directory:

Do calculations on plain text files. Executables include:

• abscissas: Generates the abscissas of a set.
• autoCorrelation: Auto-correlation of a variable.
• averageSets: Average a group of sets with a prefix.
• collect: Collect a group of sets with a prefix.
• gaussianKernelClamped: Gaussian kernal smoothing of a graph with a clamp at the average.
• gaussianKernel: Gaussian kernal smoothing of a graph.
• gaussianKernelProj: Gaussian kernal smoothing of a graph with a clamp at the average and zeroed.
• runningAvg: Running average of sets.
• skipError: Set error to zero every Nth data point.
• splitSets2: Split sets into multiple graphs.
• splitSets: Split sets into multiple graphs.
• sumSeries: Sum a series of sets into a single graph.
• sumSets: Bin values by the x column into averages of the y column.
• wham2: Weigted Histogram Analysis Method for free energies with an offset.
• wham: Weigted Histogram Analysis Method for free energies.

./analysis/asciiMod directory:

Do a function style calculation on command line input. Executables include:

• isoApex: Calculates the angle between two legs within a given stride length. Useful for continuumSphereAndVesicle.

./analysis/xyzMod directory:

Do operations on xyz files. Executables include:

• frameSkip: Only output every Nth frame.
• framesSeperate: Seperate frames into seperate XYZ files.
• move: Move all the particles by some offset.
• noType: Remove the type and header information. Generates x y and z coordinates only.
• oneTypeCount: Count all of one type.
• oneType: Output only one type.
• oneTypeFrames: Output only one type for frames.
• opticalReduction: Removes hidden particles?
• radiusTube: Radial density of a tube.
• rmFrames: Removes certain frames.
• selectFrames: Select a frame for output.
• selectRange: Select a range of frames for output.
• slice: Slices an XYZ file along an axis.
• sortFrames: Sort particles in frame by type. Useful if particle types change frequently.
• sphereMask: Masks a spherical range for output.
• target: Rescale an XYZ file from another format (ddscat?).
• xyzToBinary: Turns the XYZ file into a binary file. Can shrink files, but need binaryToXyz to make this work properly.

./include/system.h

This file includes just one class: Blob. This is the molecular dynamics system blob of parameters and data. It works with Revalee's, et al., model. Usually, you will create a blob with a real/floating type:

	Blob<double> system;

After which, you would populate it by simply setting values, with the setNAME() or addNAME() member functions, or by a script. Once they are set, you can read the values back with the readNAME() or getNAME() functions. Set and read prefixes indicate single valued parameters. Add and get prefixes indicate multi-valued parameters, and get usually returns a pointer. Getting the size of a system is as simple as:

	threeVector<double> size=system.readSize();

The important member functions are as follows:

Parameters

• Blob(); //Constructor called everytime you create a new system.
• molecule<T, fourVector > * addMolecule(molecule<T, fourVector > &value); //Add a molecule residue to the system.
• molecule<T, fourVector > * setMolecule(molecule<T,fourVector > &value, int index); //Set or change a molecule residue in the system.
• molecule<T, fourVector > * delMolecule(int index); //Delete a molecule residue in the system.
• molecule<T, fourVector > * getMolecule(); //Return the pointer to the molecule residues in the system.
• void addParticle(position pos, threeVector vel, threeVector acc); //Add a particle to the system. Includes the whole initial state for equations of motion.
• void setParticle(int index, position pos, threeVector vel, threeVector acc); //Set or change a particle in the system.
• void delParticle(int index); //Delete a particle in the system.
• void allocParticle(int n); //Allocate some particles in the system. This is here to reduce excessive allocations.
• position * getPositions(); //Get the pointer to the positions of particles in the system.
• threeVector * getVelocities(); //Get the pointer to the velocities of the particles in the system.
• threeVector * getAccelerations(); //Get the pointer to the accelerations of the particles in the system.
• T * addTwoBodyFconst(T value); //Add a non-bonded force constant to the system.
• void setTwoBodyFconst(int index, T value); //Set or change a non-bonded force constant in the system.
• T * delTwoBodyFconst(int index); //Delete a non-bonded force constant in the system.
• T * getTwoBodyFconst(); //Get a pointer to the non-bonded force constants in the system.
• T * addTwoBodyUconst(T value); //Add a non-bonded potential constant to the system.
• void setTwoBodyUconst(int index, T value); //Set or change a non-bonded potential constant in the system.
• T * delTwoBodyUconst(int index); //Delete a non-bonded potential constant in the system.
• T * getTwoBodyUconst(); //Get a pointer to the non-bonded potential constants in the system.
• int readNParticles();//Read the number of particles in the system.
• int readNMolecules();//Read the number of molecular residues in the system.
• T readGamma();//Read gamma for the Langevin thermostat.
• T readInitialTemp();//Read the initial temperature of the system, in reduced units.
• T readFinalTemp();//Read the final temperature of the system, in reduced units.
• int readSeed();//Read the random number seed of the system.
• int readNTypes();//Read the number of particle types in the system.
• threeVector readPeriodic();//Read the periodic boundaries flag in the system.
• T readCutoff();//Read the force and potential cutoff of the non-bonded interactions.
• threeVector readSize();//Read the size of the system, in reduced units.
• T readInitialTime();//Read the initial time of the system, in tau.
• T readFinalTime();//Read the ending time of the system, in tau.
• T readDeltaT();//Read the timestep of the system, in tau.
• T readStoreInterval();//Read the store interval of the system, in tau.
• T readMeasureInterval();//Read the measure interval of the system, in tau.
• T readDeltaLXY();//Read the maximum step size of the constant pressure length change, in reduced units.
• T readRemoveSolvent();//Read the amount of solvent to remove, as a fraction of total solvent.
• T readTempStepInterval();//Read temperature step interval.
• twoVector readSolventGamma();//Read solvent gamma.
• T readGammaType(int type);//Read gamma type.
• T readTension();//Read constant tension parameter.
• void setGamma(T value);//Set or change gamma.
• void setInitialTemp(T value);//Set or change the initial temperature, in reduced units.
• void setFinalTemp(T value);//Set or change the final temperature, in reduced units.
• void setSeed(int value);//Set or change the random number seed.
• void setNTypes(int value);//Set or change the number of particle types.
• void setPeriodic(threeVector value);//Set or change the periodic boundaries flag.
• void setCutoff(T value);//Set or change the non-bonded cutoff.
• void setSize(threeVector value);//Set or change the system size, in reduced units.
• void setInitialTime(T value);//Set or change the initial time, in tau.
• void setFinalTime(T value);//Set or change the final time, in tau.
• void setDeltaT(T value);//Set or change the timestep, in tau.
• void setStoreInterval(T value);//Set or change the store interval, in tau.
• void setMeasureInterval(T value);//Set or change the measure interval, in tau.
• void setDeltaLXY(T value);//Set or change the maximum step size of the constant pressure length change, in reduced units.
• void setRemoveSolvent(T value);//Set or change the fraction of solvent removal, as a fraction of total solvent.
• void setTempStepInterval(T value);//Set temperature step interval.
• void setSolventGamma(twoVector value);//Set solvent gamma.
• void setTension(T value);//Set constant tension parameter

Functions

• void doForce(int i, int j, threeVector &minImg);//Non-bonded force function between particles i and j. Utilizing the minimum image for boundaries.
• T doPotential(int i, int j, threeVector &minImg);//Non-bonded potential function between particles i and j. Utilizing the minimum image for boundaries.
• void doChainForce(int i);//Do CHAIN force bonded interactions on residue i. CHAIN is a combination of two and three body bonded forces.
• void doTorsionForce(int i);//Do TORSION force bonded interactions on residue i.
• void doBondForce(int i);//Do BOND force bonded interactions on residue i.
• void doBendForce(int i);//Do BEND force bonded interactions on residue i.
• void doBeadForce(int i);//Do BEAD force bonded interactions on residue i.
• void doBoundaryForce(int i);//Do BOUNDARY force on some particles in residue i
• fourVector doBeadNeighbors(int i);//Extract neighbor info
• std::vector<threeVector > doBeadChain(int i); //look for bead chains
• T doChainPotential(int i);//Return the CHAIN potential for residue i.
• T doDihedralPotential(int i);//Return the DIHEADRAL potential for residue i.
• T doTorsionPotential(int i);//Return the Torsion Potential for residue i.
• T doBondPotential(int i);//Return the Bond potential for residue i.
• T doBendPotential(int i);//Return the Bend potential for residue i.
• T doBeadPotential(int i);//Return the Bead potential for residue i.
• T doBoundaryPotential(int i);//Return the BOUNDARY potential on some particles in residue i.
• T doChainDPotential(int i, threeVector aSize);//Return the change in CHAIN potential for residue i when the size changes to a new state.
• T doDihedralDPotential(int i, threeVector aSize);//Return the change in DIHEADRAL potential for residue i when the size changes to a new state.
• T doTorsionDPotential(int i, threeVector aSize);//Return the change in Torsion potential for residue i when the size changes to a new state.
• T doBondDPotential(int i, threeVector aSize);//Return the change in Bond potential for residue i when the size changes to a new state.
• T doBendDPotential(int i, threeVector aSize);//Return the change in Bend potential for residue i when the size changes to a new state.
• T doBeadDPotential(int i, threeVector aSize);//Return the change in Bead potential for residue i when the size changes to a new state.