Biomolecular simulations can simulate nano- or microsecond time scales. Unfortunately, many biological processes take place in significantly longer time scales. In order to make such simulations possible it is necessary to apply enhanced sampling methods. In our group we developed a method called flying Gaussian method [1]. The studied system is simulated in multiple replicas by this method. Replicas with similar states of the system (e.g. similar conformations) repulse each other forcing the system to sample various states. Free energy of the simulated system can be obtained from sampling and from onergis by which replicas influence each other.
In order to further extend sampling we combined flying Gaussian method with parallel tempering. Each replica is simulated at different temperature. Every 1 ps a exchange of coordinates is attempted in a pair of replicas. Here we present the design of the method as well as preliminary results of its application.
1. Šućur, Z. and Spiwok, V. J. Chem. Theory Comput. 2016, 12(9), 4644-4650.