DsDNA persistence length: Difference between revisions
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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): | ||
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> | ||
--> | --> | ||
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. | 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):
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, 
, . Using an exponential fit to these data, one can find the persistence length.