Documentation - Revision history

Doye: /* Configuration file */

2022-04-19T11:40:27Z

Configuration file

← Older revision		Revision as of 11:40, 19 April 2022
Line 226:		Line 226:
	after this header, each row contains position of the centre of mass, orientation, velocity and angular velocity of a single nucleotide in the following order:		after this header, each row contains position of the centre of mass, orientation, velocity and angular velocity of a single nucleotide in the following order:

	<math>\overbrace{r_x r_y r_z}^{\rm centre-of-mass\,\, position\,\, r} \underbrace{b_x b_y b_z}_{\rm ~~Backbone-~~base\,\, vector\,\, a_1} \overbrace{n_x n_y n_z}^{\rm base\,\, normal\,\, vector\,\, a_3} \underbrace{v_x v_y v_z}_{\rm Velocity} \overbrace{L_x L_y L_z}^{\rm Angular\,\, velocity}</math>		<math>\overbrace{r_x r_y r_z}^{\rm centre-of-mass\,\, position\,\, r} \underbrace{b_x b_y b_z}_{\rm base\,\, vector\,\, a_1} \overbrace{n_x n_y n_z}^{\rm base\,\, normal\,\, vector\,\, a_3} \underbrace{v_x v_y v_z}_{\rm Velocity} \overbrace{L_x L_y L_z}^{\rm Angular\,\, velocity}</math>

	<math>a_1</math>, <math>a_2=a_3\times a_1</math> and <math>a_3</math> define a set of axes that allow you to calculate the position of all interaction sites relative to the centre of mass. See ''Geometry of the model'' section below.		<math>a_1</math>, <math>a_2=a_3\times a_1</math> and <math>a_3</math> define a set of axes that allow you to calculate the position of all interaction sites relative to the centre of mass. See ''Geometry of the model'' section below.

Doye: /* Configuration file */

2022-04-19T11:25:15Z

Configuration file

← Older revision		Revision as of 11:25, 19 April 2022
Line 226:		Line 226:
	after this header, each row contains position of the centre of mass, orientation, velocity and angular velocity of a single nucleotide in the following order:		after this header, each row contains position of the centre of mass, orientation, velocity and angular velocity of a single nucleotide in the following order:

	<math>\overbrace{r_x r_y r_z}^{\rm centre-of-mass\,\, position\,\, r} \underbrace{b_x b_y b_z}_{\rm Backbone-base\,\, vector\,\, a_1} \overbrace{n_x n_y n_z}^{\rm base normal\,\, vector\,\, a_3} \underbrace{v_x v_y v_z}_{\rm Velocity} \overbrace{L_x L_y L_z}^{\rm Angular\,\, velocity}</math>		<math>\overbrace{r_x r_y r_z}^{\rm centre-of-mass\,\, position\,\, r} \underbrace{b_x b_y b_z}_{\rm Backbone-base\,\, vector\,\, a_1} \overbrace{n_x n_y n_z}^{\rm base\,\, normal\,\, vector\,\, a_3} \underbrace{v_x v_y v_z}_{\rm Velocity} \overbrace{L_x L_y L_z}^{\rm Angular\,\, velocity}</math>

	<math>a_1</math>, <math>a_2=a_3\times a_1</math> and <math>a_3</math> define a set of axes that allow you to calculate the position of all interaction sites relative to the centre of mass. See ''Geometry of the model'' section below.		<math>a_1</math>, <math>a_2=a_3\times a_1</math> and <math>a_3</math> define a set of axes that allow you to calculate the position of all interaction sites relative to the centre of mass. See ''Geometry of the model'' section below.

Doye: /* Configuration file */

2022-04-19T11:24:25Z

Configuration file

← Older revision		Revision as of 11:24, 19 April 2022
Line 228:		Line 228:
	<math>\overbrace{r_x r_y r_z}^{\rm centre-of-mass\,\, position\,\, r} \underbrace{b_x b_y b_z}_{\rm Backbone-base\,\, vector\,\, a_1} \overbrace{n_x n_y n_z}^{\rm base normal\,\, vector\,\, a_3} \underbrace{v_x v_y v_z}_{\rm Velocity} \overbrace{L_x L_y L_z}^{\rm Angular\,\, velocity}</math>		<math>\overbrace{r_x r_y r_z}^{\rm centre-of-mass\,\, position\,\, r} \underbrace{b_x b_y b_z}_{\rm Backbone-base\,\, vector\,\, a_1} \overbrace{n_x n_y n_z}^{\rm base normal\,\, vector\,\, a_3} \underbrace{v_x v_y v_z}_{\rm Velocity} \overbrace{L_x L_y L_z}^{\rm Angular\,\, velocity}</math>

	<math>a_1</math>, <math>a_2=a_3\times a_1</math> and <math>a_3</math> define a set of axes that allow you to calculate the position of all interaction sites relative to the centre of mass. See Geometry of model section below.		<math>a_1</math>, <math>a_2=a_3\times a_1</math> and <math>a_3</math> define a set of axes that allow you to calculate the position of all interaction sites relative to the centre of mass. See ''Geometry of the model'' section below.

	===Topology file===		===Topology file===

Doye: /* Configuration file */

2022-04-19T11:21:14Z

Configuration file

← Older revision		Revision as of 11:21, 19 April 2022
Line 228:		Line 228:
	<math>\overbrace{r_x r_y r_z}^{\rm centre-of-mass\,\, position\,\, r} \underbrace{b_x b_y b_z}_{\rm Backbone-base\,\, vector\,\, a_1} \overbrace{n_x n_y n_z}^{\rm base normal\,\, vector\,\, a_3} \underbrace{v_x v_y v_z}_{\rm Velocity} \overbrace{L_x L_y L_z}^{\rm Angular\,\, velocity}</math>		<math>\overbrace{r_x r_y r_z}^{\rm centre-of-mass\,\, position\,\, r} \underbrace{b_x b_y b_z}_{\rm Backbone-base\,\, vector\,\, a_1} \overbrace{n_x n_y n_z}^{\rm base normal\,\, vector\,\, a_3} \underbrace{v_x v_y v_z}_{\rm Velocity} \overbrace{L_x L_y L_z}^{\rm Angular\,\, velocity}</math>

	<math>a_1</math>, <math>a_2=a_3\times a_1</math> and <math>a_3</math> define a set of axes that allow you to calculate the position of all interaction sites relative to the centre of mass. See [[Geometry of model]]		<math>a_1</math>, <math>a_2=a_3\times a_1</math> and <math>a_3</math> define a set of axes that allow you to calculate the position of all interaction sites relative to the centre of mass. See Geometry of model section below.

	===Topology file===		===Topology file===

Doye: /* Configuration file */

2022-04-19T11:20:21Z

Configuration file

← Older revision		Revision as of 11:20, 19 April 2022
Line 228:		Line 228:
	<math>\overbrace{r_x r_y r_z}^{\rm centre-of-mass\,\, position\,\, r} \underbrace{b_x b_y b_z}_{\rm Backbone-base\,\, vector\,\, a_1} \overbrace{n_x n_y n_z}^{\rm base normal\,\, vector\,\, a_3} \underbrace{v_x v_y v_z}_{\rm Velocity} \overbrace{L_x L_y L_z}^{\rm Angular\,\, velocity}</math>		<math>\overbrace{r_x r_y r_z}^{\rm centre-of-mass\,\, position\,\, r} \underbrace{b_x b_y b_z}_{\rm Backbone-base\,\, vector\,\, a_1} \overbrace{n_x n_y n_z}^{\rm base normal\,\, vector\,\, a_3} \underbrace{v_x v_y v_z}_{\rm Velocity} \overbrace{L_x L_y L_z}^{\rm Angular\,\, velocity}</math>

	<math>a_1</math>, <math>a_2=a_3\times a_1</math> and <math>a_3</math> define a set of axes that allow you to calculate the position of all interaction sites relative to the centre of mass.		<math>a_1</math>, <math>a_2=a_3\times a_1</math> and <math>a_3</math> define a set of axes that allow you to calculate the position of all interaction sites relative to the centre of mass. See [[Geometry of model]]

	===Topology file===		===Topology file===

Doye: /* Geometry of the Model */

2022-04-19T11:19:18Z

Geometry of the Model

← Older revision		Revision as of 11:19, 19 April 2022
Line 302:		Line 302:
	In the configuration/trajectory files only the positions and orientations of the nucleotides are stored. If one wants to recover the positions of the individual interaction sites in the model, some maths need to be done.		In the configuration/trajectory files only the positions and orientations of the nucleotides are stored. If one wants to recover the positions of the individual interaction sites in the model, some maths need to be done.

	The position of the ~~interactin~~ sites can be recovered as follows:		The position of the interaction sites can be recovered as follows:

	In oxDNA1:		In oxDNA1:

Doye: /* Configuration file */

2022-04-19T11:18:20Z

Configuration file

← Older revision		Revision as of 11:18, 19 April 2022
Line 229:		Line 229:

	<math>a_1</math>, <math>a_2=a_3\times a_1</math> and <math>a_3</math> define a set of axes that allow you to calculate the position of all interaction sites relative to the centre of mass.		<math>a_1</math>, <math>a_2=a_3\times a_1</math> and <math>a_3</math> define a set of axes that allow you to calculate the position of all interaction sites relative to the centre of mass.

	~~In oxDNA1:~~

	~~Hydrogen-bonding/repulsion site within the base <math>=r+0.4\, a_1</math>~~

	~~Stacking site within the base <math>= r+0.34\,a_1</math>~~

	~~Backbone repulsion site <math>= r-0.4\, a_1 </math>~~

	~~In oxDNA2:~~

	~~Hydrogen-bonding site within the base <math>= r+0.4\, a_1</math>~~

	~~Stacking site within the base <math>= r+0.34\, a_1</math>~~

	~~Backbone repulsion site <math>= r-0.34\, a_1+0.3408\, a_2</math>~~

	===Topology file===		===Topology file===

Doye: /* Geometry of the Model */

2022-04-19T11:17:36Z

Geometry of the Model

← Older revision		Revision as of 11:17, 19 April 2022
Line 335:		Line 335:

	Backbone repulsion site <math>= r-0.34\, a_1+0.3408\, a_2</math>		Backbone repulsion site <math>= r-0.34\, a_1+0.3408\, a_2</math>


	The picture in the [[Model_introduction\|introduction]] might help understanding where the sites are.		The picture in the [[Model_introduction\|introduction]] might help understanding where the sites are.

Doye: /* Geometry of the Model */

2022-04-19T11:17:24Z

Geometry of the Model

← Older revision		Revision as of 11:17, 19 April 2022
Line 318:		Line 318:
	In the configuration/trajectory files only the positions and orientations of the nucleotides are stored. If one wants to recover the positions of the individual interaction sites in the model, some maths need to be done.		In the configuration/trajectory files only the positions and orientations of the nucleotides are stored. If one wants to recover the positions of the individual interaction sites in the model, some maths need to be done.

	The position of the ~~base, stacking and backbone~~ sites can be recovered as follows:		The position of the interactin sites can be recovered as follows:

	~~base site~~: ~~(center) + 0.40 * (axis vector)~~		In oxDNA1:

	~~stacking~~ site: ~~(center)~~ + 0.34 * (axis vector)		Hydrogen-bonding/repulsion site within the base <math>=r+0.4\, a_1</math>

			Stacking site within the base <math>= r+0.34\,a_1</math>

			Backbone repulsion site <math>= r-0.4\, a_1 </math>

			In oxDNA2:

			Hydrogen-bonding site within the base <math>= r+0.4\, a_1</math>

			Stacking site within the base <math>= r+0.34\, a_1</math>

			Backbone repulsion site <math>= r-0.34\, a_1+0.3408\, a_2</math>

	~~backbone site: (center) - 0.40 * (axis_vector)~~

	The picture in the [[Model_introduction\|introduction]] might help understanding where the sites are.		The picture in the [[Model_introduction\|introduction]] might help understanding where the sites are.

Doye: /* Configuration file */

2022-04-19T11:14:38Z

Configuration file

← Older revision		Revision as of 11:14, 19 April 2022
Line 231:		Line 231:

	In oxDNA1:		In oxDNA1:

	Hydrogen-bonding/repulsion site within the base <math>=r+0.4\, a_1</math>		Hydrogen-bonding/repulsion site within the base <math>=r+0.4\, a_1</math>
	Stacking site within the base = r+a1*0.34
	Backbone repulsion site = r-a1*0.4		Stacking site within the base <math>= r+0.34\,a_1</math>

			Backbone repulsion site <math>= r-0.4\, a_1 </math>

	In oxDNA2:		In oxDNA2:
	Hydrogen-bonding site within the base = r+a1*0.4
	Stacking site within the base = r+a1*0.34		Hydrogen-bonding site within the base <math>= r+0.4\, a_1</math>
	Backbone repulsion site = r-a10.34+a20.3408
			Stacking site within the base <math>= r+0.34\, a_1</math>

			Backbone repulsion site <math>= r-0.34\, a_1+0.3408\, a_2</math>

	===Topology file===		===Topology file===