Added unique base pairing (f96520ff) · Commits · 郑智淋 / lammps

examples/USER/cgdna/README

+17 −0

Original line number	Diff line number	Diff line
		@@ -55,6 +55,23 @@ are sequence-dependent (cf. keyword 'seqdep' in according pair styles).

		/******************************************************************************/

		/examples/oxDNA2/unique_bp:

		This example uses atom types 1-8 to model a 13 base pair duplex.
		The nucleotide types are assigned as follows:
		A = 1,5; C = 2,6; G = 3,7; T = 4,8
		When a large number of atom types is used, this feature allows
		quasi-unique base pairing between two individual nucleotides.

		The topology is
		A C G T A C G T A C G T A
		1 - 2 - 3 - 4 - 5 - 6 - 7 - 8 - 1 - 2 - 7 - 8 - 1
		\| \| \| \| \| \| \| \| \| \| \| \| \|
		4 - 3 - 2 - 1 - 8 - 7 - 6 - 5 - 4 - 3 - 6 - 5 - 4
		T G C A T G C A T G C A T

		/******************************************************************************/

		/examples/oxRNA2/duplex4

		This is the duplex2 run with the oxRNA2 force field instead of the oxDNA or

examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.4type

0 → 100644

+130 −0

Original line number	Diff line number	Diff line
		# LAMMPS data file
		26 atoms
		26 ellipsoids
		24 bonds

		4 atom types
		1 bond types

		# System size
		-20.000000 20.000000 xlo xhi
		-20.000000 20.000000 ylo yhi
		-20.000000 20.000000 zlo zhi

		# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
		Atoms

		1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1
		2 2 -4.957432645895970e-01 -3.379920348381733e-01 3.897628551303122e-01 1 1 1
		3 3 -2.192046146198370e-01 -5.585242491865227e-01 7.795257102606244e-01 1 1 1
		4 4 1.335125603737887e-01 -5.849567473090943e-01 1.169288565390937e+00 1 1 1
		5 1 4.398311230978960e-01 -4.081036426625517e-01 1.559051420521249e+00 1 1 1
		6 2 5.932984957350773e-01 -8.942535970570469e-02 1.948814275651561e+00 1 1 1
		7 3 5.405813207414517e-01 2.603302434705350e-01 2.338577130781873e+00 1 1 1
		8 4 3.000000000000002e-01 5.196152422706634e-01 2.728339985912185e+00 1 1 1
		9 1 -4.483805615185452e-02 5.983222783087083e-01 3.118102841042497e+00 1 1 1
		10 2 -3.740938811152403e-01 4.690988894808181e-01 3.507865696172809e+00 1 1 1
		11 3 -5.733436834716847e-01 1.768531046465427e-01 3.897628551303121e+00 1 1 1
		12 4 -5.733436834716849e-01 -1.768531046465427e-01 4.287391406433434e+00 1 1 1
		13 1 -3.740938811152403e-01 -4.690988894808182e-01 4.677154261563746e+00 1 1 1
		14 4 3.740938811152403e-01 4.690988894808182e-01 4.677154261563746e+00 2 1 1
		15 1 5.733436834716849e-01 1.768531046465427e-01 4.287391406433434e+00 2 1 1
		16 2 5.733436834716849e-01 -1.768531046465426e-01 3.897628551303122e+00 2 1 1
		17 3 3.740938811152403e-01 -4.690988894808181e-01 3.507865696172810e+00 2 1 1
		18 4 4.483805615185462e-02 -5.983222783087085e-01 3.118102841042498e+00 2 1 1
		19 1 -3.000000000000003e-01 -5.196152422706636e-01 2.728339985912186e+00 2 1 1
		20 2 -5.405813207414519e-01 -2.603302434705351e-01 2.338577130781874e+00 2 1 1
		21 3 -5.932984957350776e-01 8.942535970570474e-02 1.948814275651561e+00 2 1 1
		22 4 -4.398311230978962e-01 4.081036426625520e-01 1.559051420521249e+00 2 1 1
		23 1 -1.335125603737888e-01 5.849567473090947e-01 1.169288565390937e+00 2 1 1
		24 2 2.192046146198373e-01 5.585242491865231e-01 7.795257102606246e-01 2 1 1
		25 3 4.957432645895974e-01 3.379920348381736e-01 3.897628551303123e-01 2 1 1
		26 4 6.000000000000006e-01 0.000000000000000e+00 1.110223024625157e-16 2 1 1

		# Atom-ID, translational, rotational velocity
		Velocities

		1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		11 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		12 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		13 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		14 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		15 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		16 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		17 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		18 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		19 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		20 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		21 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		22 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		23 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		24 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		25 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		26 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00

		# Atom-ID, shape, quaternion
		Ellipsoids

		1 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		2 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.555728057861408e-01 0.000000000000000e+00 0.000000000000000e+00 2.947551744109042e-01
		3 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 8.262387743159949e-01 0.000000000000000e+00 0.000000000000000e+00 5.633200580636221e-01
		4 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 6.234898018587335e-01 0.000000000000000e+00 0.000000000000000e+00 7.818314824680299e-01
		5 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 3.653410243663950e-01 0.000000000000000e+00 0.000000000000000e+00 9.308737486442042e-01
		6 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 7.473009358642424e-02 0.000000000000000e+00 0.000000000000000e+00 9.972037971811802e-01
		7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -2.225209339563144e-01 0.000000000000000e+00 0.000000000000000e+00 9.749279121818237e-01
		8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -5.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 8.660254037844387e-01
		9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 7.330518718298263e-01 -0.000000000000000e+00 0.000000000000000e+00 -6.801727377709196e-01
		10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.009688679024190e-01 -0.000000000000000e+00 0.000000000000000e+00 -4.338837391175581e-01
		11 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.888308262251286e-01 -0.000000000000000e+00 0.000000000000000e+00 -1.490422661761745e-01
		12 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.888308262251286e-01 0.000000000000000e+00 0.000000000000000e+00 1.490422661761745e-01
		13 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.009688679024190e-01 0.000000000000000e+00 0.000000000000000e+00 4.338837391175582e-01
		14 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 -4.338837391175582e-01 9.009688679024190e-01 0.000000000000000e+00
		15 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -1.490422661761746e-01 9.888308262251286e-01 0.000000000000000e+00
		16 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 1.490422661761745e-01 9.888308262251286e-01 -0.000000000000000e+00
		17 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 4.338837391175581e-01 9.009688679024190e-01 -0.000000000000000e+00
		18 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 6.801727377709192e-01 7.330518718298267e-01 0.000000000000000e+00
		19 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.660254037844386e-01 5.000000000000001e-01 0.000000000000000e+00
		20 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.749279121818235e-01 2.225209339563145e-01 0.000000000000000e+00
		21 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.972037971811801e-01 -7.473009358642428e-02 0.000000000000000e+00
		22 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.308737486442041e-01 -3.653410243663952e-01 0.000000000000000e+00
		23 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 7.818314824680296e-01 -6.234898018587339e-01 0.000000000000000e+00
		24 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.633200580636215e-01 -8.262387743159952e-01 0.000000000000000e+00
		25 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -2.947551744109044e-01 9.555728057861407e-01 0.000000000000000e+00
		26 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 -0.000000000000000e+00

		# Bond topology
		Bonds

		1 1 1 2
		2 1 2 3
		3 1 3 4
		4 1 4 5
		5 1 5 6
		6 1 6 7
		7 1 7 8
		8 1 8 9
		9 1 9 10
		10 1 10 11
		11 1 11 12
		12 1 12 13
		13 1 14 15
		14 1 15 16
		15 1 16 17
		16 1 17 18
		17 1 18 19
		18 1 19 20
		19 1 20 21
		20 1 21 22
		21 1 22 23
		22 1 23 24
		23 1 24 25
		24 1 25 26

examples/USER/cgdna/examples/oxDNA2/unique_bp/data.duplex4.8type

0 → 100644

+130 −0

Original line number	Diff line number	Diff line
		# LAMMPS data file
		26 atoms
		26 ellipsoids
		24 bonds

		8 atom types
		1 bond types

		# System size
		-20.000000 20.000000 xlo xhi
		-20.000000 20.000000 ylo yhi
		-20.000000 20.000000 zlo zhi

		# Atom-ID, type, position, molecule-ID, ellipsoid flag, density
		Atoms

		1 1 -6.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 1 1 1
		2 2 -4.957432645895970e-01 -3.379920348381733e-01 3.897628551303122e-01 1 1 1
		3 3 -2.192046146198370e-01 -5.585242491865227e-01 7.795257102606244e-01 1 1 1
		4 4 1.335125603737887e-01 -5.849567473090943e-01 1.169288565390937e+00 1 1 1
		5 5 4.398311230978960e-01 -4.081036426625517e-01 1.559051420521249e+00 1 1 1
		6 6 5.932984957350773e-01 -8.942535970570469e-02 1.948814275651561e+00 1 1 1
		7 7 5.405813207414517e-01 2.603302434705350e-01 2.338577130781873e+00 1 1 1
		8 8 3.000000000000002e-01 5.196152422706634e-01 2.728339985912185e+00 1 1 1
		9 1 -4.483805615185452e-02 5.983222783087083e-01 3.118102841042497e+00 1 1 1
		10 2 -3.740938811152403e-01 4.690988894808181e-01 3.507865696172809e+00 1 1 1
		11 7 -5.733436834716847e-01 1.768531046465427e-01 3.897628551303121e+00 1 1 1
		12 8 -5.733436834716849e-01 -1.768531046465427e-01 4.287391406433434e+00 1 1 1
		13 1 -3.740938811152403e-01 -4.690988894808182e-01 4.677154261563746e+00 1 1 1
		14 4 3.740938811152403e-01 4.690988894808182e-01 4.677154261563746e+00 2 1 1
		15 5 5.733436834716849e-01 1.768531046465427e-01 4.287391406433434e+00 2 1 1
		16 6 5.733436834716849e-01 -1.768531046465426e-01 3.897628551303122e+00 2 1 1
		17 3 3.740938811152403e-01 -4.690988894808181e-01 3.507865696172810e+00 2 1 1
		18 4 4.483805615185462e-02 -5.983222783087085e-01 3.118102841042498e+00 2 1 1
		19 5 -3.000000000000003e-01 -5.196152422706636e-01 2.728339985912186e+00 2 1 1
		20 6 -5.405813207414519e-01 -2.603302434705351e-01 2.338577130781874e+00 2 1 1
		21 7 -5.932984957350776e-01 8.942535970570474e-02 1.948814275651561e+00 2 1 1
		22 8 -4.398311230978962e-01 4.081036426625520e-01 1.559051420521249e+00 2 1 1
		23 1 -1.335125603737888e-01 5.849567473090947e-01 1.169288565390937e+00 2 1 1
		24 2 2.192046146198373e-01 5.585242491865231e-01 7.795257102606246e-01 2 1 1
		25 3 4.957432645895974e-01 3.379920348381736e-01 3.897628551303123e-01 2 1 1
		26 4 6.000000000000006e-01 0.000000000000000e+00 1.110223024625157e-16 2 1 1

		# Atom-ID, translational, rotational velocity
		Velocities

		1 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		2 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		3 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		4 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		5 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		6 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		7 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		8 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		9 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		10 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		11 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		12 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		13 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		14 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		15 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		16 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		17 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		18 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		19 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		20 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		21 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		22 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		23 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		24 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		25 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		26 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00

		# Atom-ID, shape, quaternion
		Ellipsoids

		1 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
		2 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.555728057861408e-01 0.000000000000000e+00 0.000000000000000e+00 2.947551744109042e-01
		3 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 8.262387743159949e-01 0.000000000000000e+00 0.000000000000000e+00 5.633200580636221e-01
		4 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 6.234898018587335e-01 0.000000000000000e+00 0.000000000000000e+00 7.818314824680299e-01
		5 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 3.653410243663950e-01 0.000000000000000e+00 0.000000000000000e+00 9.308737486442042e-01
		6 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 7.473009358642424e-02 0.000000000000000e+00 0.000000000000000e+00 9.972037971811802e-01
		7 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -2.225209339563144e-01 0.000000000000000e+00 0.000000000000000e+00 9.749279121818237e-01
		8 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -5.000000000000001e-01 0.000000000000000e+00 0.000000000000000e+00 8.660254037844387e-01
		9 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 7.330518718298263e-01 -0.000000000000000e+00 0.000000000000000e+00 -6.801727377709196e-01
		10 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.009688679024190e-01 -0.000000000000000e+00 0.000000000000000e+00 -4.338837391175581e-01
		11 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.888308262251286e-01 -0.000000000000000e+00 0.000000000000000e+00 -1.490422661761745e-01
		12 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.888308262251286e-01 0.000000000000000e+00 0.000000000000000e+00 1.490422661761745e-01
		13 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 9.009688679024190e-01 0.000000000000000e+00 0.000000000000000e+00 4.338837391175582e-01
		14 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 -4.338837391175582e-01 9.009688679024190e-01 0.000000000000000e+00
		15 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -1.490422661761746e-01 9.888308262251286e-01 0.000000000000000e+00
		16 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 1.490422661761745e-01 9.888308262251286e-01 -0.000000000000000e+00
		17 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 4.338837391175581e-01 9.009688679024190e-01 -0.000000000000000e+00
		18 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 6.801727377709192e-01 7.330518718298267e-01 0.000000000000000e+00
		19 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 8.660254037844386e-01 5.000000000000001e-01 0.000000000000000e+00
		20 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.749279121818235e-01 2.225209339563145e-01 0.000000000000000e+00
		21 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.972037971811801e-01 -7.473009358642428e-02 0.000000000000000e+00
		22 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 9.308737486442041e-01 -3.653410243663952e-01 0.000000000000000e+00
		23 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 7.818314824680296e-01 -6.234898018587339e-01 0.000000000000000e+00
		24 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 0.000000000000000e+00 5.633200580636215e-01 -8.262387743159952e-01 0.000000000000000e+00
		25 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 -2.947551744109044e-01 9.555728057861407e-01 0.000000000000000e+00
		26 1.173984503142341e+00 1.173984503142341e+00 1.173984503142341e+00 -0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 -0.000000000000000e+00

		# Bond topology
		Bonds

		1 1 1 2
		2 1 2 3
		3 1 3 4
		4 1 4 5
		5 1 5 6
		6 1 6 7
		7 1 7 8
		8 1 8 9
		9 1 9 10
		10 1 10 11
		11 1 11 12
		12 1 12 13
		13 1 14 15
		14 1 15 16
		15 1 16 17
		16 1 17 18
		17 1 18 19
		18 1 19 20
		19 1 20 21
		20 1 21 22
		21 1 22 23
		22 1 23 24
		23 1 24 25
		24 1 25 26

examples/USER/cgdna/examples/oxDNA2/unique_bp/generate_unique.py

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examples/USER/cgdna/examples/oxDNA2/unique_bp/in.duplex4.4type

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