Empirical potential Monte Carlo simulation of fluid structure

Soper, A. K.

doi:10.1016/0301-0104(95)00357-6

Cited by 710 publications

(667 citation statements)

References 12 publications

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“…In structure based coarse graining, a CG potential is determined in such a way that predefined target functions, which structurally characterize the system, are reproduced in the CG simulation. In the iterative Boltzmann inversion method 37 …”

Section: Coarse Grained Potentialsmentioning

confidence: 99%

Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites

Rzepiela

Louhivuori

Peter

et al. 2011

Phys. Chem. Chem. Phys.

191

198

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Hybrid simulations, in which part of the system is represented at atomic resolution and the remaining part at a reduced, coarse-grained, level offer a powerful way to combine the accuracy associated with the atomistic force fields to the sampling speed obtained with coarse-grained (CG) potentials. In this work we introduce a straightforward scheme to perform hybrid simulations, making use of virtual sites to couple the two levels of resolution. With the help of these virtual sites interactions between molecules at different levels of resolution, i.e. between CG and atomistic molecules, are treated the same way as the pure CG-CG interactions. To test our method, we combine the Gromos atomistic force field with a number of coarse-grained potentials, obtained through several approaches that are designed to obtain CG potentials based on an existing atomistic model, namely iterative Boltzmann inversion, force matching, and a potential of mean force subtraction procedure (SB). We also explore the use of the MARTINI force field for the CG potential. A simple system, consisting of atomistic butane molecules dissolved in CG butane, is used to study the performance of our hybrid scheme. Based on the potentials of mean force for atomistic butane in CG solvent, and the properties of 1 : 1 mixtures of atomistic and CG butane which should exhibit ideal mixing behavior, we conclude that the MARTINI and SB potentials are particularly suited to be combined with the atomistic force field. The MARTINI potential is subsequently used to perform hybrid simulations of atomistic dialanine peptides in both CG butane and water. Compared to a fully atomistic description of the system, the hybrid description gives similar results provided that the dielectric screening of water is accounted for. Within the field of biomolecules, our method appears ideally suited to study e.g. protein-ligand binding, where the active site and ligand are modeled in atomistic detail and the rest of the protein, together with the solvent, is coarse-grained.

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Section: Coarse Grained Potentialsmentioning

confidence: 99%

Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites

Rzepiela

Louhivuori

Peter

et al. 2011

Phys. Chem. Chem. Phys.

191

198

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“…To the best of our knowledge, several techniques such as Reverse Monte Carlo (RMC) [9] and Empirical Potential Structural Refinement (EPSR) [10] have been recently developed to obtain structural models of glasses from diffraction data. An alternative approach to the gallate glasses is to use Molecular Dynamics (MD) simulation techniques [11,12] to produce distribution function or diffraction patterns that can be compared directly with the experimental data.…”

Section: Introductionmentioning

confidence: 99%

Structural investigation of gallate glass using L3-edge extended X-ray absorption spectroscopy and computer simulation

Kidkhunthod

Bootchanont

Barnes³

2016

Journal of Non-Crystalline Solids

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General rightsThis document is made available in accordance with publisher policies. Please cite only the published version using the reference above. ) prepared by aerodynamic levitation and laser heating. The short range ordering around the rare-earth has been obtained by combined technique including molecular dynamics simulation (MD). The results give an average Pr-O coordination number of 6.68(2) and a mean Ga-O coordination number of 4.29(2).A good agreement between the experimental data and the simple molecular dynamics simulations give rising a glass network of a Pr-O polyhedral structure and a predominant GaO 4 tetrahedral network in this glass.

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“…Figure 1 shows the experimental neutron diffraction data which were fitted using the empirical potential structure refinement (EPSR) technique. 8,9 The differences between the three experimental diffraction datasets in Figure 1 are caused by the different neutron scattering properties of 1 H and D, and this information is used by EPSR to produce a representative 3D structural model consistent with the experimental diffraction data (further details are provided in the ESI). 10, 11 The structural analysis of the EPSR-derived model shown in Figure 1 is carried out by calculating intermolecular paircorrelation functions such as g C-H (r, , ) which gives the probability of the position of the H atom of a 2 nd molecule with respect to the C atom of the reference molecule.…”

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confidence: 99%

Polar stacking of molecules in liquid chloroform

et al. 2015

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Empirical potential Monte Carlo simulation of fluid structure

Cited by 710 publications

References 12 publications

Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites

Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites

Structural investigation of gallate glass using L3-edge extended X-ray absorption spectroscopy and computer simulation

Polar stacking of molecules in liquid chloroform

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