RNA model: Difference between revisions

Revision as of 16:38, 10 March 2014

The RNA model, oxRNA, treats each RNA nucleotide as a single rigid body with multiple interaction sites, following the coarse-graining apporach adopted for the DNA model. The nucleotides interact with pairwise interaction potentials, which are schematically illustrated below: [[Image::Image_duplex_combined_annotated.png]]

Backbone connectivity $V_{\rm {backbone}}$ ,
Excluded volume $V_{\rm {exc}}$ ,
Hydrogen bonding $V_{\rm {H.B.}}$ ,
Nearest-neighbour stacking $V_{\rm {stack}}$ ,
Cross-stacking between base-pair steps in a duplex $V_{crossst.}$ ,
Coaxial stacking $V_{\rm {cxstack}}$ .

which are schematically illustrated in the picture:

Simulation units

The code uses dimensionless energy, mass, length and timescales for convenience. The relationship between simulation units (SU) and SI units is given below.

Simulation unit	Physical unit
1 unit of length	8.518x10 $^{-10}$ m
1 unit of energy	4.142x10 $^{-20}$ J
1 unit of temperature	3000 K
1 unit of force	4.863x10 $^{-11}$ N
1 unit of mass	5.34x10 $^{-25}$ kg
1 unit of time	3.06x10 $^{-12}$ s

The oxRNA model is integrated into the oxDNA simulation code. In particular, it is possible to use Virtual Move Monte Carlo (VMMC), Monte Carlo (MC) and Molecular Dynamics (MD) simulation algorithms using the same format of input file as for the DNA model, with the following additional line included in the input file to specify RNA model:

interaction_type = RNA

The RNA model comes with two parametrizations, the average-base and sequence-dependent one. In the average-base parametrization, the $V_{\rm {H.B.}}$ interaction strengths are the same for all Watson-Crick and wobble base pairs (AU, GC, GU) and 0 for all other types of base pairs. The interaction strengths have the same strength for all possible pairs of nucleotides interacting with stacking interaction $V_{\rm {stack}}$ . In the sequence-dependent version of the model, the interaction strengths of $V_{\rm {stack}}$ and $V_{\rm {H.B.}}$ depend on the type of interacting bases.

The average-base parametrization is used by default. In order to use the sequence-dependent version of the model, the following options need to be added into the input file:

use_average_seq = 0
seq_dep_file = rna_sequence_dependent_parameters.txt

Note that the file rna_sequence_dependent_parameters.txt needs to be located in the directory where you run the simulation, or full location of the file needs to be specified in seq_dep_file option.

Furthermore, the configuration files need to be generated so that the nucleotides are positioned so that they satisfy RNA potentials (for instance in the case of duplex, they need to be initialized in an A-helical structure). For this purpose, a script generate-RNA.py is provided in UTILS/ subdirectory of the source code main directory. For instance, if one wants to generate an initial configuration of three strands, two of them complementary (with sequence 3'-GCAAGUCG-5' and its complementary) and in a duplex configuration, and one single strand with sequence 3'-ACCCGU-5', one needs to create the following file text file, called for example sekvences.txt:

DOUBLE GCAAGUCG
ACCCGU

./generate-RNA.py <files_with_sequence> prefix [box = 20]

./generate-RNA.py <files_with_sequence> prefix [box = 20]

The model and its performance is discussed in detail in the following reference:

P. Šulc, F. Romano, T. E. Ouldridge, J. P. K. Doye, A. A. Louis: A nucleotide-level coarse-grained model of RNA, submitted

@@ Line 4: / Line 4: @@
 #Backbone connectivity <math>V_{\rm backbone}</math>,
-#Excluded volume ,
+#Excluded volume <math>V_{\rm exc}</math>,
-#Hydrogen bonding,
+#Hydrogen bonding <math>V_{\rm  H.B.}</math>,
-#Nearest-neighbour stacking,
+#Nearest-neighbour stacking <math>V_{\rm stack}</math>,
-#Cross-stacking between base-pair steps in a duplex,
+#Cross-stacking between base-pair steps in a duplex <math>V_{cross st.}</math>,
-#Coaxial stacking.
+#Coaxial stacking <math>V_{\rm cx stack}</math>.
 which are schematically illustrated in the picture:
 [[Image:Image_duplex_combined_annotated.png|500px]]
@@ Line 37: / Line 36: @@
 |-
 | 1 unit of mass
-| 1.66x10<math>^{-25}</math> kg
+| 5.34x10<math>^{-25}</math> kg
 |-
 | 1 unit of time
-| 1.71x10<math>^{-12}</math> s
+| 3.06x10<math>^{-12}</math> s
 |-
 |}
-The model and its performance is discussed in detail in the following references (the thesis provides the most complete analysis):
+The oxRNA model is integrated into the oxDNA simulation code. In particular, it is possible to use Virtual Move Monte Carlo (VMMC), Monte Carlo (MC) and Molecular Dynamics (MD) simulation algorithms using the same format of input file as for the DNA model, with the following additional line included in the input file to specify RNA model:
+<pre>
+interaction_type = RNA
+</pre>
+The RNA model comes with two parametrizations, the average-base and sequence-dependent one. In the average-base parametrization, the <math>V_{\rm  H.B.}</math> interaction strengths are the same for all Watson-Crick and wobble base pairs (AU, GC, GU) and 0 for all other types of base pairs. The interaction strengths have the same strength for all possible pairs of nucleotides interacting with stacking interaction <math>V_{\rm stack}</math>.
+In the sequence-dependent version of the model, the interaction strengths of <math>V_{\rm stack}</math> and <math>V_{\rm H.B.}</math> depend on the type of interacting bases.
+The average-base parametrization is used by default. In order to use the sequence-dependent version of the model, the following options need to be added into the input file:
+<pre>
+use_average_seq = 0
+seq_dep_file = rna_sequence_dependent_parameters.txt
+</pre>
+Note that the file <tt>rna_sequence_dependent_parameters.txt</tt> needs to be located in the directory where you run the simulation, or full location of the file needs to be specified in <tt>seq_dep_file</tt> option.
+Furthermore, the configuration files need to be generated so that the nucleotides are positioned so that they satisfy RNA potentials (for instance in the case of duplex, they need to be initialized in an A-helical structure). For this purpose, a script  <tt>generate-RNA.py</tt> is provided in <tt>UTILS/</tt> subdirectory of the source code main directory.
+For instance, if one wants to generate an initial configuration of three strands, two of them complementary (with sequence 3'-GCAAGUCG-5' and its complementary) and in a duplex configuration, and one single strand with sequence 3'-ACCCGU-5', one needs to create the following file text file, called for example <tt>sekvences.txt</tt>:
+<pre>
+DOUBLE GCAAGUCG
+ACCCGU
+</pre>
+<pre>
+./generate-RNA.py <files_with_sequence> prefix [box = 20]
+</pre>
-T. E. Ouldridge, D.Phil. Thesis, University of Oxford, 2011.
+./generate-RNA.py <files_with_sequence> prefix [box = 20]
-[http://ora.ox.ac.uk/objects/uuid:b2415bb2-7975-4f59-b5e2-8c022b4a3719 Coarse-grained modelling of DNA and DNA self-assembly]
-T. E. Ouldridge, A. A. Louis and J. P. K. Doye, J. Chem. Phys, 134, 085101 (2011)
+The model and its performance is discussed in detail in the following reference:
-[http://link.aip.org/link/?JCP/134/085101 Structural, mechanical and thermodynamic properties of a coarse-grained DNA model] ([http://arxiv.org/abs/arXiv:1009.4480 arXiv])
-P. Šulc, F. Romano, T. E. Ouldridge, L. Rovigatti, J. P. K. Doye, A. A. Louis, ''J. Chem. Phys.'' '''137''', 135101 (2012)
+P. Šulc, F. Romano, T. E. Ouldridge, J. P. K. Doye, A. A. Louis: A nucleotide-level coarse-grained model of RNA, submitted
-[http://jcp.aip.org/resource/1/jcpsa6/v137/i13/p135101_s1 Sequence-dependent thermodynamics of a coarse-grained DNA model] ([http://arxiv.org/abs/1207.3391 arxiv])

RNA model: Difference between revisions

Revision as of 16:38, 10 March 2014

Simulation units

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