Difference between revisions of "DsDNA persistence length"

From OxDNA
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The example shows how to calculate a persistence length of a double stranded DNA molecule.  
 
The example shows how to calculate a persistence length of a double stranded DNA molecule.  
 
dsDNA persistence length. The persistence length in this example is calculated using the following formula (see [http://jcp.aip.org/resource/1/jcpsa6/v134/i8/p085101_s1?bypassSSO=1] for details):
 
dsDNA persistence length. The persistence length in this example is calculated using the following formula (see [http://jcp.aip.org/resource/1/jcpsa6/v134/i8/p085101_s1?bypassSSO=1] for details):
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http://www-thphys.physics.ox.ac.uk/people/PetrSulc/images/eqn.png
  
 
<!-- <math>\langle {\bf n_k} \cdot {\bf n_0} \rangle = \exp(- k \langle l_0 \rangle /L_{ps}).
 
<!-- <math>\langle {\bf n_k} \cdot {\bf n_0} \rangle = \exp(- k \langle l_0 \rangle /L_{ps}).
 
</math>
 
</math>
 
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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:
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<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, <math> \langle {\bf n_k} \cdot {\bf n_0} \rangle </math>. Using an exponential fit to these data, one can find the persistence length.
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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> -->. Using an exponential fit to these data, one can find the persistence length.

Revision as of 19:19, 17 April 2012

Persistence length of a double-stranded DNA

The example shows how to calculate a persistence length of a double stranded DNA molecule. dsDNA persistence length. The persistence length in this example is calculated using the following formula (see [1] for details):

eqn.png


In the EXAMPLES/PERSISTENCE_LENGTH 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:

oxDNA input_persistence

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:

dspl.py trajectory.dat init.top 10 50

This program will produce a table of correlations between helical vectors, eqn2.png, . Using an exponential fit to these data, one can find the persistence length.