General-purpose Coarse-grained
Molecular Dynamics Program

COGNAC(COarse-Grained molecular dynamics program by NAgoya Cooperation)

Takeshi Aoyagi
JCII, Doi project0 sec-3 msec

GOURMET-6 μsec

MUFFINSUSHI-9 nsec

PASTA-12 psec

COGNAC-15 fsec
-15
fm

-12
pm

-9nm

-6μm

-3mm

0m

Coarse-grained model
A set of atoms are represented by
one dynamical unit
XXX

United atom model– A methylene (CH2) unit isrepresented by single mass point
Gay-Berne potential model– A rigid part of molecule is representedby single ellipsoid
Bead-spring model– Several monomer units are represented
by single bead (mass point)

General-purpose
X General computational models and potentialfunctions
X General objectives< Features and functions of COGNAC >X Basic function of molecular dynamics/mechanics
X Potential functions for coarse-grained model
X Flexible modeling
X Extended functions and tools for analysis
X New functions for zooming
X Extensibility of the program
X User interface

Molecular Dynamics/Molecular Mechanics
XXX

Molecular dynamics (MD)– Ensembles» NVE» NVT,NPH,NPT(loose-coupling / extended Hamiltonian methods)
Langevin dynamics
Molecular mechanics (MM)– Steepest descent / conjugate gradient methods

Potential Functions for Coarse-grained Models
XXX

Bonding– 2-body(bond):Harmonic,Morse,FENE,Gaussian,Polynomial,Table– 3-body(angle):Theta harmonic,Cosine harmonic
Theta polynomial,Table– 4-body(torsion):Cosine polynomial,Table
Non-bonding pair interaction– Lennard-Jones,Gay-Berne,LJ-GB, Table
Electrostatic– Coulomb interaction(Ewald,Reaction field)– Dipole-dipole interaction (Reaction field)

Example of Application:
Gay-Berne - Lennard-Jones hybrid potential
N CCH2H2C CH2H2C CH3nCB(4-methyl-4’-cyanobiphenyl)

Smectic phase(non-polar model)

EllipsoidSphere
Nematic phase(polar model)

Modeling molecular architectures using
SILK (1)XXX

SILK is a tool to generate molecular architectures for
COGNACSILK is written in Python and used on GOURMETSILK has basic functions and template functions.
– Basic functions define atoms, bonds, angles, torsions.
They are used to generate molecules with complex
architectures– Template functions are used to generate simple polymer
molecules such as homopolymers and blockcopolymers

Modeling molecular architectures using
SILK (2)
XAn example of the usage of the basic functions
name="mol"numMol=10
self.engine.createMolecule(name)for i in range(0, 4):self.engine.addAtoms(name, "UA", "UA_PE")
for i in range(0, 3):self.engine.addBonds(name, i, i+1, "BOND_PE")
for i in range(0, 2):self.engine.addAngles(name, i, i+1, i+2, "ANGLE_PE")
for i in range(0, 1):
self.engine.addTorsions(name, i, i+1, i+2, i+3, "TORSION_PE")
for i in range(0, 4):self.engine.addInteractionSites(name, [i], "NB_PE", "PAIR")
self.engine.setSystem(name, numMol)

Modeling molecular architectures using
SILK (3)
XAn example of the usage of the template functions

name="A20B40A20"
numMol=50
key="LINEAR"
sequence=[("A",20),("B",40),("A",20)]
atomType={"A":"atom1", "B":"atom2"}
bondType={"A_A":"bond1", "A_B":"bond3", "B_B":"bond2"}
interactionSiteType={"A":"siteType1", "B":"siteType2"}
self.engine.makeBeadSpringPolym(name, numMol, key, sequence, atomType,bondType, interactionSiteType)Modeling molecular architectures using“Action” SILKX

Running SILK by “Action” on GOUMET

Selectionof diblock

Notes: This function is released
as a gift without documents

Analysis tools
XPython scripts for the analysis of COGNAC output– Basic analysis» Distance, angle, torsion» Radius of gyration, etc.
– Geometry analysis» Pair distribution functions» Orientation order parameters etc.
– Trajectory analysis» Mean square displacements» Correlation function of normal coordinates etc.

Example of Application ：Topological gel
Crosslink withchemical bond

Crosslink withring

Feature of topological gel
・High degree of swelling・High elasticity
・High clarity
Physical gel

Chemical gel

Topological gel

Snapshot structure during elongation

Generation of initial coordinates
X

Generation by COGNAC– Random: Amorphous like structures– Helix: Helical structures at regular lattice points– Crystal: Crystal structures defined by crystal data, i.e.
unit lattice, symmetric operation and fractional
coordinates– Semi-crystalline lamella: Semi-crystalline lamellastructures consisting of a crystal phase and an
amorphous phase– Multi phase structure: Micro/macro phase-separetedstructures of block copolymer/polymer blend obtained
by SUSHI

Data conversion of molecular structure fromother file formats
XConversion from mol/PDB format file to UDF file

mol format file displayedby WebLab ViewerLite(TM)Converted data to UDF displayed
by GOURMET

Data conversion of molecular structure toother file formats
X

Conversion from UDF file to PDB/car/XYZ format file

UDF file displayed
by GOURMET

car format file displayedby WebLab ViewerLite(TM)Additional functions for studying mechanicalproperties of materials
XXX

External field and deformation– Homogeneous field, e.g. electric fields– Shear flow by the Lees-Edwards boundary conditions– Unit cell deformation
Solid wall
– Flat wall
– Structured wall
Bond creation/scission– Simple model for chemical reaction

Example of Application :Clay(laponite) - Polymer(PEO) composite
Network structure of clay-polymer is observed in water.
Clay plates order under shear flow.

Example of Application:
Confined polymer melts under shear flow
Polymer melts
confined betweenwalls. Apply shear
flow by sliding thewalls.
20nm

20nm

Example of Application: Network formation

Reaction among two andthree functional monomers

New Functions for Zooming
X Density biased Monte Carlo (DBMC)
X Density biased potential (DBP)– Embedding polymer chain into multiphasestructures obtained by SUSHI
X Staggered reflective boundary condition (SRBC)– Boundary conditions for simulating interfacial
structure of polymer blends
X Lamella builder– Generation of semi-crystalline lamellastructures

Example of Application:
ABA triblock copolymer
A lamella structureof ABA triblock
copolymer.
Loop/bridge ratio
obtained by the SCF
calculation(SUSHI)
is reproduced.

Example of Application:
Elastic behavior of ABA triblock copolymer
Strain‑stress curve

0.6BCC sphere phase

Stress [ε σ ‑3]

0.5
0.4
0.3
0.2
0.1
0.0
‑0.1
0100

200

300

Strain [%]300% Strain

400500

Example of Application:
Interface of Polymer Blend
Interfacial structure ofA/B polymer blendd ε 0 /d t=2.08x10 ‑3 τ ‑1

1.20

Thick‑ δinterfaceelongation
ε N=0.0‑ δ ε N=0.3‑ δ ε N=1.4‑ δ ε N=10.0‑3Elongation bydeforming the unit cellStress̲zz [ε σ ]

1.00
0.80

Thin interface

0.60
0.40
0.20
0.00
00.1

0.2

0.3

Strain0.40.5

Example of Application:
Semi-crystalline lamella

6nm

A semi-crystalline
lamella structure of theunited atom model ofalkane
The distribution of thelength and loop/bridge
ratio in amorphous phaseare determined by mean
field theory
A snapshot duringelongation

elongation

User defined potential functions
COGNAC is written in C++
X COGNAC has classes for the templates of user defined
potentials
XX

Users can define
a functional formand parameters ina template function#include "userbond1.h"
double UserBond1::calcforce(const Vector3d& dr,Vector3d& ftmp){
double r,delR,ene,tmp;
r=dr.length();delR=r-r0;
tmp=kconst*delR;
ftmp=dr*(tmp/r);
ene=0.5*tmp*delR;
return ene;}

Example of user defined dynamics andpotential functions: DPD
X

Equations of motion and potential functions ofdissipative particle dynamics (DPD)
dridv i= vi ,= fidtdt

fi = ∑ (FijC + FijD + FijR )i≠ jaij (1 − rij )rˆij
F =0Cij(r < 1),(r ≥ 1)
ij

ij

FijD = −γwD (rij )(rˆij ⋅ v ij )rˆij , FijR = σwR (rij )θij rˆij

Display of molecular structures
XMolecuar structures can be displayed by using “Action”
tools or Python scripts– Arbitrary set of molecules/atoms/bonds can be displayed

Displaying all molecules of ABA
triblock copolymers in a lamella
phase

Displaying only A type atoms and single
bridge chain.

Analysis using “Action” on GOURMETX

Some of the analysis toolscan be launched by“Action” on GOURMETPlot of the results : Density profiles

Plot of the results : Stress-strain curveHelpX

Brief comments oneach UDF structure
and parameter are
displayedHELP

Unit conversion
Unit of each parametercan be converted toarbitrary units
X if COGNAC UDF has unit
parameters,i.e.
reduced mass in [amu]reduced energy in [kJ/mol]
reduced length in [nm].
X

COGNAC:Linking to other layers
Elastic modulus ofsingle component

MUFFINχ parameters

SUSHI

Friction constant,
MePASTAInteraction
parameters

Non-equilibriumstructure

COGNAC
Polymer structure

Multi-phase structure,
Interaction parametersSummary
X COGNAC has following functions:– Basic functions for MD/MM– Versatile functions for molecular modeling– Various potential functions and ensembles forcoarse-grained models– Various functions and tools for material
design– New functions for zooming– Extensibility of program

X

Developers of COGNAC– T.Aoyagi, F.Sawa, T.Shoji, H.Fukunaga(JCII, Doi project)– Prof. J.Takimoto (Nagoya Univ.)