Avoiding a Pitfall in Dynamically Optimized Monte Carlo Method
This paper examines a problem that might occur during the equilibration phase in simulations using the Dynamically Optimized Monte Carlo Method (DOMC) , a method for the simulation of anisotropic and inhomogeneous systems such as biological molecules. A criterion to detect the problem is presented along with an extension of DOMC to improve performance of the method during equilibration. The improved DOMC method is shown to perform well on test cases.
KeywordsEquilibrium Position Biological Molecule Dynamically Optimize Minimal Potential Energy Inhomogeneous System
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