A script to extract helical axis and calculate ‘writhe’ from an AMBER trajectory of circular DNA.
SerraLINE calculates bending angles at different length scales from the global molecular contour of MD simulations of DNA. This molecular contour needs to be first calculated by WrLINE.
Program to analyse flexibility properties at different length scales from MD simulations of DNA. It allows to observe how flexibility arises from local fluctuations, with the option of inferring global elastic constants that describe the molecule’s overall flexibility.