I simulate this model by Espresso, The results were near to the paper
results, but there was a little problem. Grouping the neighborhood base pairs in
condensed material simulations. Due to simulate interaction among base pairs A_T
C_G I used lj none bonded feature. It was based on the referenced paper. But it is not suitable. My substituted model : Using fene bond with the nearest neighbor base pair. And delete it when another base pair particle goes to nearer than the past particle and make a new bond and ......... I forced to use fene bond because this feature is not designed for none bonded potentials .....
It made my code so slow because I implemented it by tcl coding .... I try to find a suitable feature perhaps designed in the past.