Optimization of replica exchange molecular dynamics by fast mimicking.
We present an approach to mimic replica exchange molecular dynamics simulations (REMD) on a microsecond time scale within a few minutes rather than the years, which would be required for real REMD. The speed of mimicked REMD makes it a useful tool for "testing" the efficiency of different settings for REMD and then to select those settings, that give the highest efficiency. We present an optimization approach with the example of Hamiltonian REMD using soft-core interactions on two model systems, GTP and 8-Br-GTP. The optimization process using REMD mimicking is very fast. Optimization of Hamiltonian-REMD settings of GTP in explicit water took us less than one week. In our study we focus not only on finding the optimal distances between neighboring replicas, but also on finding the proper placement of the highest level of softness. In addition we suggest different REMD simulation settings at this softness level. We allow several replicas to be simulated at the same Hamiltonian simultaneously and reduce the frequency of switching attempts between them. This approach allows for more efficient conversions from one stable conformation to the other.
Leiden Amsterdam Center for Drug Research (LACDR), Division of Molecular Toxicology, Vrije Universiteit, Amsterdam, The Netherlands.
Jozef
J
Hritz
Chris
C
Oostenbrink
D003198:Computer Simulation; D006160:Guanosine Triphosphate / Q000031:analogs & derivatives / Q000737:chemistry*; D008956:Models, Chemical; D008968:Molecular Conformation; D011789:Quantum Theory; D013696:Temperature; D013997:Time Factors
D006160:Guanosine Triphosphate