COGNACのコンセプト \(COarse Grained molecular dynamics program developed by NAgoya Cooperation\)
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1 COGNAC (COarse-Grained molecular dynamics program by NAgoya Cooperation) ( ),
2 0 sec -3 msec -6 sec -9 nsec -12 psec -15 fsec GOURMET SUSHI PASTA COGNAC MUFFIN fm pm nm m mm m
3 United atom model (CH 2 ) Gay-Berne potential model Bead-spring model
4
5 Molecular dynamics (MD) Ensembles»NVE» NVT,NPH,NPT (loose-coupling / extended Hamiltonian methods) Langevin dynamics Molecular mechanics (MM) Steepest descent / conjugate gradient methods
6 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)
7 : Gay-Berne - Lennard-Jones hybrid potential C CH 2 H 2 C CH 2 H 2 C CH 3 ncb (4-methyl-4 -cyanobiphenyl) Ellipsoid Sphere Smectic phase(non-polar model) Nematic phase(polar model)
8 SILK (1) SILK COGNAC SILK Python GOURMET SILK
9 SILK (2) 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)
10 SILK (3) 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)
11 Action SILK gift Action GOUMET SILK Selection of diblock
12
13 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 lamella structures consisting of a crystal phase and an amorphous phase Multi phase structure: Micro/macro phase-separeted structures of block copolymer/polymer blend obtained by SUSHI
14 mol/pdb UDF WebLab ViewerLite (TM) mol GOURMET UDF
15 UDF PDB/car/XYZ GOURMET UDF WebLab ViewerLite (TM) car
16 etc. Lees-Edwards MD»
17 Clay(laponite) - Polymer(PEO) composite clay-polymer Clay
18 20nm 20nm
19
20 Density biased Monte Carlo (DBMC) Density biased potential (DBP) SUSHI Staggered reflective boundary condition (SRBC) Lamella builder
21 ABA triblock copolymer ABA triblock copolymer SUSHI Loop/Bridge
22 ABA triblock copolymer 300% Strain BCC sphere phase εσ
23 A/B εσ ε τ elongation δε δε δε δε
24 6nm elongation
25 COGNAC C++ COGNAC UserBond1, UserAngle1 #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;
26 DPD Dissipative particle dynamics (DPD) dr dt i dv = vi, dt i = f i f i F C ij = ( C D R F + + ) ij Fij Fij i j aij = 0 ( 1 r ) ( < ) ij rˆ ij rij ( r 1) ij 1, F D ij D = w ( )( ) R R r ( ) ij rˆ ij vij rˆ ij, Fij = w rij ijrˆ ij
27 Action Python molecules/atoms/bonds ABA triblock copolymers A
28 COGNAC Python»»»»»»
29 GOURMET Action GOURMET Action
30 :
31 : -
32 UDF HELP
![COGNAC UDF unit parameters reduced mass in [amu]](/docs-images/78/78557703/images/33-1.jpg "reduced energy in [kj/mol] reduced length in [nm].")
33 COGNAC UDF unit parameters reduced mass in [amu] reduced energy in [kj/mol] reduced length in [nm].
34 COGNAC: χ MUFFIN SUSHI PASTA COGNAC
35 COGNAC : MD/MM
36 COGNAC JCII
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![3 3.1 R r r + R R r Rr [ ] ˆn(r) = ˆn(r + R) (3.1) R R = r ˆn(r) = ˆn(0) r 0 R = r C nn (r, r ) = C nn (r + R, r + R) = C nn (r r, 0) (3.2) ( 2.2 ) C](/thumbs/94/119172213.jpg "3 3.1 R r r + R R r Rr [ ] ˆn(r) = ˆn(r + R) (3.1) R R = r ˆn(r) = ˆn(0) r 0 R = r C nn (r, r ) = C nn (r + R, r + R) = C nn (r r, 0) (3.2) ( 2.2 ) C")
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