The usability of vsites for GROMACS simulation on DNA strands and AWH analysis

Sammanfattning

Molecular dynamic simulations provide a better understanding of what occurs in macromolecules such as in biomolecules by capturing the motion of the structure and its interactions. To maximize the time used of a supercomputer on a simulation the use of virtual sites is useful. Especially for DNA-helices which have not been explored with the virtual sites. The A and B conformations were explored with multiple combinations of A, T, C and G helices as well as a Dickerson dodecamer DNA-helix which show that it is possible to use virtual sites with the available force field as well as use the virtual site containing DNA-helix for analyses, such as accelerated weighted histogram analysis.