DsDNA persistence length - Revision history

Snodinb: /* Persistence length of a double-stranded DNA */

2014-10-08T11:34:07Z

Persistence length of a double-stranded DNA

← Older revision		Revision as of 11:34, 8 October 2014
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	Note that for calculating a persistence length of a dsDNA, one needs a large number of decorrelated states. To obtain the states (which will be saved into a trajectory file), run the simulation program using the prepared input_persistence file:		Note that for calculating a persistence length of a dsDNA, one needs a large number of decorrelated states. To obtain the states (which will be saved into a trajectory file), run the simulation program using the prepared input_persistence file:

	<pre>oxDNA input_persistence</pre>		<pre>../../bin/oxDNA input_persistence</pre>

	The program will run a molecular dynamics simulation at 23 °C and record the individual configurations. By default, they are saved in the <tt>trajectory.dat</tt> file. To analyze the data, use the python script <tt>dspl.py</tt>:		The program will run a molecular dynamics simulation at 23 °C and record the individual configurations. By default, they are saved in the <tt>trajectory.dat</tt> file. To analyze the data, use the python script <tt>dspl.py</tt>:

	<pre>dspl.py trajectory.dat init.top 10 50</pre>		<pre>./dspl.py trajectory.dat init.top 10 50</pre>

	This program will produce a table of correlations between helical vectors, http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/eqn2.png.		This program will produce a table of correlations between helical vectors, http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/eqn2.png.

Romano at 09:35, 18 May 2012

2012-05-18T09:35:40Z

← Older revision		Revision as of 09:35, 18 May 2012
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	http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/ds.png		http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/ds.png

	The exponential fit shows, in this particular example, a persistence length of 124.8 base pairs. ~~[[Cadnano]]~~		The exponential fit shows, in this particular example, a persistence length of 124.8 base pairs.

Romano at 10:58, 14 May 2012

2012-05-14T10:58:51Z

← Older revision		Revision as of 10:58, 14 May 2012
Line 23:		Line 23:
	http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/ds.png		http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/ds.png

	The exponential fit shows, in this particular example, a persistence length of 124.8 base pairs. [Cadnano]		The exponential fit shows, in this particular example, a persistence length of 124.8 base pairs. [[Cadnano]]

Romano: /* Persistence length of a double-stranded DNA */

2012-05-14T10:58:35Z

Persistence length of a double-stranded DNA

← Older revision		Revision as of 10:58, 14 May 2012
Line 23:		Line 23:
	http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/ds.png		http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/ds.png

	The exponential fit shows, in this particular example, a persistence length of 124.8 base pairs.		The exponential fit shows, in this particular example, a persistence length of 124.8 base pairs. [Cadnano]

Rovigatti: /* Persistence length of a double-stranded DNA */

2012-04-21T17:08:46Z

Persistence length of a double-stranded DNA

← Older revision		Revision as of 17:08, 21 April 2012
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	<pre>oxDNA input_persistence</pre>		<pre>oxDNA input_persistence</pre>

	The program will run a molecular dynamics simulation at 23 °C and record the individual configurations. ~~They~~ are saved in trajectory.dat file. To analyze the data, use the python script dspl.py:		The program will run a molecular dynamics simulation at 23 °C and record the individual configurations. By default, they are saved in the <tt>trajectory.dat</tt> file. To analyze the data, use the python script <tt>dspl.py</tt>:

	<pre>dspl.py trajectory.dat init.top 10 50</pre>		<pre>dspl.py trajectory.dat init.top 10 50</pre>

Rovigatti: /* Persistence length of a double-stranded DNA */

2012-04-21T17:07:47Z

Persistence length of a double-stranded DNA

← Older revision		Revision as of 17:07, 21 April 2012
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	http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/eqn.png		http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/eqn.png

	In the <tt> EXAMPLES/PERSISTENCE_LENGTH </tt> directory, you will find a setup for calculating the persistence length of a 202 base pairs long dsDNA.		In the <tt> EXAMPLES/PERSISTENCE_LENGTH</tt> directory, you will find a setup for calculating the persistence length of a 202 base pairs long dsDNA.
	Note that for calculating a persistence length of a dsDNA, one needs a large number of decorrelated states. To obtain the states (which will be saved into a trajectory file), run the simulation program using the prepared input_persistence file:		Note that for calculating a persistence length of a dsDNA, one needs a large number of decorrelated states. To obtain the states (which will be saved into a trajectory file), run the simulation program using the prepared input_persistence file:

Line 18:		Line 18:
	This program will produce a table of correlations between helical vectors, http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/eqn2.png.		This program will produce a table of correlations between helical vectors, http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/eqn2.png.

	The program dspl.py requires base.py in the UTILS directory to be present and to have UTILS directory set in your PYTHONPATH environment variable. The program calculates the local helical axis vector (n_k) as a unit vector pointing from the midpoint of hydrogen bonding sites of k-th base pair to the midpoint between (k+1)-th base pair.		The program <tt>dspl.py</tt> requires <tt>base.py</tt> in the UTILS directory to be present and to have UTILS directory set in your PYTHONPATH environment variable. The program calculates the local helical axis vector (n_k) as a unit vector pointing from the midpoint of hydrogen bonding sites of k-th base pair to the midpoint between (k+1)-th base pair.
	The init.top file contains topology of the 202 base pairs long strand (included in the <tt> EXAMPLES/PERSISTENCE_LENGTH </tt>). In the example above, the program starts at the 10-th base pair and calculates correlations of n_10 with n_11, n_12, etc. up to n_60. It then prints out the correlations (one per line). Using an exponential fit to these data, one can find the persistence length, as illustrated in the following picture:		The init.top file contains topology of the 202 base pairs long strand (included in the <tt> EXAMPLES/PERSISTENCE_LENGTH</tt>). In the example above, the program starts at the 10-th base pair and calculates correlations of n_10 with n_11, n_12, etc. up to n_60. It then prints out the correlations (one per line). Using an exponential fit to these data, one can find the persistence length, as illustrated in the following picture:

	http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/ds.png		http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/ds.png

	The exponential fit shows, in this particular example, a persistence length of 124.8 base pairs.		The exponential fit shows, in this particular example, a persistence length of 124.8 base pairs.

Rovigatti: /* Persistence length of a double-stranded DNA */

2012-04-21T17:06:59Z

Persistence length of a double-stranded DNA

← Older revision		Revision as of 17:06, 21 April 2012
Line 23:		Line 23:
	http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/ds.png		http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/ds.png

	The exponential fit shows, in this particular example, persistence length 124.8 base pairs.		The exponential fit shows, in this particular example, a persistence length of 124.8 base pairs.

Sulc at 19:35, 17 April 2012

2012-04-17T19:35:56Z

← Older revision		Revision as of 19:35, 17 April 2012
Line 18:		Line 18:
	This program will produce a table of correlations between helical vectors, http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/eqn2.png.		This program will produce a table of correlations between helical vectors, http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/eqn2.png.

	The program dspl.py requires base.py in the UTILS directory to be present and to have UTILS directory set in your PYTHONPATH environment variable. The program calculates the local helical axis vector (n_k) as a unit vector pointing from the midpoint of hydrogen bonding sites of k-th base to the midpoint between (k+1)-th ~~bases~~.		The program dspl.py requires base.py in the UTILS directory to be present and to have UTILS directory set in your PYTHONPATH environment variable. The program calculates the local helical axis vector (n_k) as a unit vector pointing from the midpoint of hydrogen bonding sites of k-th base pair to the midpoint between (k+1)-th base pair.
	The init.top file contains topology of the 202 base pairs long strand (included in the <tt> EXAMPLES/PERSISTENCE_LENGTH </tt>). In the example above, the program starts at the 10-th base pair and calculates correlations of n_10 with n_11, n_12, etc. up to n_60. It then prints out the correlations (one per line). Using an exponential fit to these data, one can find the persistence length, as illustrated in the following picture:		The init.top file contains topology of the 202 base pairs long strand (included in the <tt> EXAMPLES/PERSISTENCE_LENGTH </tt>). In the example above, the program starts at the 10-th base pair and calculates correlations of n_10 with n_11, n_12, etc. up to n_60. It then prints out the correlations (one per line). Using an exponential fit to these data, one can find the persistence length, as illustrated in the following picture:

Sulc at 19:35, 17 April 2012

2012-04-17T19:35:24Z

← Older revision		Revision as of 19:35, 17 April 2012
Line 18:		Line 18:
	This program will produce a table of correlations between helical vectors, http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/eqn2.png.		This program will produce a table of correlations between helical vectors, http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/eqn2.png.

	The program dspl.py requires base.py in the UTILS directory to be present and to have UTILS directory set in your PYTHONPATH environment variable. The program calculates the local helical axis vector (n_k) as a unit vector pointing from the midpoint of hydrogen bonding sites of k-th base ~~pair pointing~~ to the midpoint between (k+1)-th bases.		The program dspl.py requires base.py in the UTILS directory to be present and to have UTILS directory set in your PYTHONPATH environment variable. The program calculates the local helical axis vector (n_k) as a unit vector pointing from the midpoint of hydrogen bonding sites of k-th base to the midpoint between (k+1)-th bases.
	The init.top file contains topology of the 202 base pairs long strand (included in the <tt> EXAMPLES/PERSISTENCE_LENGTH </tt>). In the example above, the program starts at the 10-th base pair and calculates correlations of n_10 with n_11, n_12, etc. up to n_60. It then prints out the correlations (one per line). Using an exponential fit to these data, one can find the persistence length, as illustrated in the following picture:		The init.top file contains topology of the 202 base pairs long strand (included in the <tt> EXAMPLES/PERSISTENCE_LENGTH </tt>). In the example above, the program starts at the 10-th base pair and calculates correlations of n_10 with n_11, n_12, etc. up to n_60. It then prints out the correlations (one per line). Using an exponential fit to these data, one can find the persistence length, as illustrated in the following picture:

Sulc at 19:34, 17 April 2012

2012-04-17T19:34:47Z

← Older revision		Revision as of 19:34, 17 April 2012
Line 17:		Line 17:

	This program will produce a table of correlations between helical vectors, http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/eqn2.png.		This program will produce a table of correlations between helical vectors, http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/eqn2.png.

	~~<!-- <math> \langle {\bf n_k} \cdot {\bf n_0} \rangle </math> -->.~~

	The program dspl.py requires base.py in the UTILS directory to be present and to have UTILS directory set in your PYTHONPATH environment variable. The program calculates the local helical axis vector (n_k) as a unit vector pointing from the midpoint of hydrogen bonding sites of k-th base pair pointing to the midpoint between (k+1)-th bases.		The program dspl.py requires base.py in the UTILS directory to be present and to have UTILS directory set in your PYTHONPATH environment variable. The program calculates the local helical axis vector (n_k) as a unit vector pointing from the midpoint of hydrogen bonding sites of k-th base pair pointing to the midpoint between (k+1)-th bases.