There are difficulties when conventional canonical-ensemble simulations are carried out for biomolecular systems. This is because the canonical simulations tend to get trapped in a local-minimum free-energy state of the biomolecular system, and sufficient sampling in the conformational space of the system is not able to be obtained. To overcome such difficulties, I had recently proposed the replica-permutation method (RPM) [1]. In RPM, replicas (or copies) of a target system are prepared, and different temperatures are assigned to the replicas. Canonical simulations at the assigned temperatures are performed individually and simultaneously. During the simulations, the temperatures are permutated among the replicas. Here, the Suwa-Todo algorithm [2] is employed for replica-permutation trials to minimize its rejection ratio. In my talk, I will show efficiency of RPM for small biomolecules. I will also show applications of the Hamiltonian RPM, which is a generalization of RPM, to amyloid β-peptides (Aβ) [3,4]. Aβs form oligomers and then amyloid fibrils which are associated with Alzheimer’s disease. I will discuss the oligomerization process of Aβs.

Reference:
[1] S. G. Itoh and H. Okumura, J. Chem. Theory Comput. 9, 570 (2013).
[2] H. Suwa and S. Todo, Phys. Rev. Lett. 105, 120603 (2010).
[3] S. G. Itoh and H. Okumura, J. Comput. Chem. 34, 2493 (2013).
[4] S. G. Itoh and H. Okumura, J. Phys. Chem. B 118, 11428 (2014).