RNA duplex melting

Introduction

This example shows how our code can be used to calculate melting temperature of an RNA duplex (8-mer) using the Virtual Move Monte Carlo (VMMC) algorithm. The corresponding files are located in the repository in subdirectory EXAMPLES/RNA_DUPLEX_MELT

Setting the order parameters and weights

The example uses umbrella sampling in order to make the sampling more efficient. In order to obtain a correct estimate of the melting temperature, the simulation has to sample many times the transitions between unbonded and bonded states. The sampling is aided by assigning weights to a particular state, specified for this example in file wfile.txt , where the first column specifies the value of order parameter (number of native bonds in the duplex in our case) and second column specifies the weight assigned to the state:

0 8.
1 16204
2 1882.94
3 359.746
4 52.5898
5 15.0591
6 7.21252
7 2.2498
8 2.89783