Incremental umbrella sampling

Details Incremental umbrella sampling Incremental umbrella sampling

2011-07-26

2011-07-26

Bullock, Jr., Lewis A (Department: 2193)

Electrical computers: arithmetic processing and calculating

Electrical digital calculating computer

Particular function performed

C708S200000

Reexamination Certificate

active

07987219

ABSTRACT:
The present invention is an incremental umbrella sampling method to improve the performance of established sampling methods. It is sampling the state space by iteratively generating statesxi,tand their weighting factors represented by Formula (a) by fitting the sampling distribution function ρj(x) of the next iteration to at least one weighted property of the already sampled states. This means that ρj(x) is fitted to the product represented by Formula (b), in which Formula (a) is the weighting factor and O(x,i) is a function respectively a property of the states xi,t. The number of states xi,tand the number of weighting factors (see Formula (a)) is incremented with each iteration. In order to have a consistent set of weighting factors (see Formula (a)), the weighting factors are recalculated in each iteration for all, respectively for a set of selected, states. By fitting ρj(x) in the state space it is possible to use all the information of Formula (a) and O(xi,t) for the states xi,tgenerated so far. The fitting step allows to use different fitting strategies. For example the fitting can bias the sampling away from areas where intensive sampling has been done in the preceding iterations, or the sampling can be directed along local gradients respectively towards local minima or maxima of one or several weighted properties. In each of the iterations, the sampling distribution function is fitted in a way to improve the overall sampling of the state space. The method supports multi-objective optimizations. State space integrals can be solved. It reduces the probability that the system is trapped. The invention is general. It can be used with different sampling methods, in particular with Monte Carlo sampling, Metropolis Monte Carlo sampling, or dynamic simulations. It can be combined with the concepts of simulated annealing and multicanonical sampling. It provides a general framework that can be adapted to the system and the observables of interest.

REFERENCES:
patent: 5148365 (1992-09-01), Dembo
Christian Bartels et al., “Multidimensional Adaptive Umbrella Sampling: Applications to Main Chain and Side Chain Peptide Conformations”, Journal of computational Chemistry, vol. 18, No. 12, pp. 1450-1462, 1997.
Christian Bartels et al., “Determination of equilibrium properties of biomolecular systems using multidimensional adaptive umbrella sampling”, Journal of Chemical Physics, vol. 111, No. 17, pp. 8048-8067, Nov. 1, 1999.
Tim N. Heinz et al., “Comparison of four methods to compute the dielectric permittivity of liquids from molecular dynamics simulations”, Journal of chemical Physics, vol. 115, No. 3, pp. 1125-1136, Jul. 15, 2001.

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