We report results from all-atom Monte Carlo simulations of the 36-residue villin headpiece subdomain HP-36. Protein-solvent interactions are approximated by an implicit solvent model. The parallel tempering is used to overcome the problem of slow convergence in low-temperature protein simulations. Our results show that this technique allows one to sample native-like structures of small proteins...

iii ACKNOWLEDGEMENTS I would like to thank my advisors Dana Randall and Eric Vigoda for their guidance and support, which they gave generously. I was fortunate to have the opportunity to work with two of the leading researchers in my field. Dana never ceased to surprise me with her quick insights and ability to get to crux of a problem. I thoroughly enjoyed working with Eric and am always inspi...

We propose a new global optimization method (Simulated Tempering) for simulating effectively a system with a rough free energy landscape (i.e. many coexisting states) at finite non-zero temperature. This method is related to simulated annealing, but here the temperature becomes a dynamic variable, and the system is always kept at equilibrium. We analyze the method on the Random Field Ising Mode...

To reduce the number of replicas required in the conventional replica exchange method for huge systems, recently the replica exchange with solute tempering (REST) method was proposed. Here we showed that a variant of REST realized by rescaling the force-field parameters can be performed with GROMACS 4 without changing the code. We tested the variant REST for alanine dipeptide and an N-terminal ...

Parallel tempering Monte Carlo and multihistogram methods are combined to study the phase changes of the water octamer. The heat capacity is calculated continuously from very low temperatures up to T5230 K. We find the melting temperature to be 178.5 K. In addition, a solid–solid phase change is found at 12 K. We introduce an order parameter to monitor this low temperature phase change. © 2001 ...