Search results for "Umbrella sampling"

Adaptive Finite Temperature String Method in Collective Variables.

2017

Here we present a modified version of the on-the-fly string method for the localization of the minimum free energy path in a space of arbitrary collective variables. In the proposed approach the shape of the biasing potential is controlled by only two force constants, defining the width of the potential along the string and orthogonal to it. The force constants and the distribution of the string nodes are optimized during the simulation, improving the convergence. The optimized parameters can be used for umbrella sampling with a path CV along the converged string as the reaction coordinate. We test the new method with three fundamentally different processes: chloride attack to chloromethane…

Stability of a Split Streptomycin Binding Aptamer

2016

Here we investigated the stability of an aptamer, which is formed by two RNA strands and binds the antibiotic streptomycin. Molecular dynamics simulations in aqueous solution confirmed the geometry and the pattern of hydrogen bond interactions that was derived from the crystal structure (1NTB). The result of umbrella sampling simulations indicated a favored streptomycin binding with a free energy of ΔGbind° = −101.7 kJ mol–1. Experimentally, the increase in oligonucleotide stability upon binding of streptomycin was probed by single-molecule force spectroscopy. Rate dependent force spectroscopy measurements revealed a decrease in the natural off-rate (koff-COMPLEX = 0.22 ± 0.16 s–1) for the …

Depletion induced isotropic-isotropic phase separation in suspensions of rod-like colloids

2007

When non-adsorbing polymers are added to an isotropic suspension of rod-like colloids, the colloids effectively attract each other via depletion forces. We performed Monte Carlo simulations to study the phase diagram of such rod-polymer mixture. The colloidal rods were modeled as hard spherocylinders; the polymers were described as spheres of the same diameter as the rods. The polymers may overlap with no energy cost, while the overlap of polymers and rods is forbidden. Large amounts of depletant cause phase separation of the mixture. We estimated the phase boundaries of isotropic-isotropic coexistence both in the bulk and in confinement. To determine the phase boundaries we applied the gra…

Suspensions of rod-like colloids and a depleting agent under confinement

2008

We present a computer simulation study of suspensions of rod-like colloids and a depletant in confinement to a slit-pore. Mixtures of hard spherocylinders and ideal spheres were studied by means of Monte Carlo simulations in the grand canonical ensemble. By use of finite size scaling analysis we determined the critical behaviour. In order to overcome large barriers in the free energy we applied the successive umbrella sampling method (Virnau and Muller 2004 J. Chem. Phys. 120 10925). We find that, under confinement, the critical point of gas–liquid demixing shifts to higher concentrations of rods and smaller concentrations of spheres due to the formation of an orientationally ordered surfac…

Monte-Carlo Methods

2003

The article conbtains sections titled: 1 Introduction and Overview 2 Random-Number Generation 2.1 General Introduction 2.2 Properties That a Random-Number Generator (RNG) Should Have 2.3 Comments about a Few Frequently Used Generators 3 Simple Sampling of Probability Distributions Using Random Numbers 3.1 Numerical Estimation of Known Probability Distributions 3.2 “Importance Sampling” versus “Simple Sampling” 3.3 Monte-Carlo as a Method of Integration 3.4 Infinite Integration Space 3.5 Random Selection of Lattice Sites 3.6 The Self-Avoiding Walk Problem 3.7 Simple Sampling versus Biased Sampling: the Example of SAWs Continued 4 Survey of Applications to Simulation of Transport Processes 4.…

A Successive Umbrella Sampling Algorithm to Sample and Overcome Free Energy Barriers

2006

Conformational equilibrium of chorismate. A QM/MM theoretical study combining statistical simulations and geometry optimisations in gas phase and in …

2003

We report a theoretical study on the conformational equilibrium of chorismate that precedes its rearrangement to prephenate, an important enzyme-catalyzed reaction. In first place we show that the usual classification of chorismate conformers based on the relative position of the hydroxyl and ether bridge, pseudo-diaxial and pseudo-diequatorial, is not the only relevant factor from the point of view of the a posteriori rearrangement. Here we also analyse another complementary geometrical classification based on the interatomic distance between the carbon atoms to be bounded. Using the umbrella sampling approach and this distance as distinguished internal reaction coordinate, the gas phase A…