Tutorials of advanced MD simulations

3.1 Large scale simulation using the parallel I/O

If a simulation system is huge, and a larger number of processors is available, it takes a significant amount of time to gather data for restart and trajectory file updates. So, it is preferred, each process writes local information separately, rather than a single does for all. In GENESIS, the parallel input/output (I/O) scheme is available to deal effectively with larger restart or trajectory files. In this tutorial, we show the example of the MD simulation with parallel I/O, using the protein crowding system with villin headpiece (The snapshot is shown below).


3.2 String method

String method is a powerful technique for searching the physically most probable pathway between two stable states whose structures are known a priori by experiments. GENESIS supports the standard algorithm of the string method. This tutorial gives step-by-step instructions for applying GENESIS’s string method to the conformational change of tri-alanine.