All-atom molecular dynamics simulation with levels of polarization
Date of Issue2015
School of Physical and Mathematical Sciences
Molecular dynamics (MD) simulation has become an indispensable tool in computational chemistry. It is believed that, to produce reliable results, polarization effect must be included in MD simulation. In this thesis, several studies with MD simulation is conducted with different levels of polarization. First, conventional molecular dynamics simulation without polarization is performed to study interactions between graphene and biomolecules. Interesting results are presented, but more fascinating phenomenon and properties cannot be explored with methods at this level. Then protein molecular dynamics simulations are performed with models representing two levels of polarization, namely fluctuating backbone charge and polarized protein-specific charge updating. The results showed that the newly developed polarized protein-specific charge updating scheme, named ERPPC was promising in several perspectives. It incorporates polarization into MD simulation by varying atomic charges periodically. Simulations show that ERPPC reproduced loop dynamics of enzyme YopH. At the same time, it only consumes about 2.5 times computing time of classical molecular dynamics simulation. Further development is expected on ERPPC to improve both accuracy and efficiency.