DREIDING:  a generic force field for molecular simulations

Mayo, Stephen L.; Olafson, Barry D.; Goddard, William A.

doi:10.1021/j100389a010

Cited by 5,761 publications

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“…Nonetheless, the CED Molecular Dynamics method is nonparametric. Beyond the predetermined force field, in our case a generic force field 16 published in 1990, CED used no adjustable parameters and no experimental input information. Moreover, in principle, the CED molecular dynamics method can make predictions, as a function of pressure and temperature, and it is general enough to deal with complex mixtures, including sol- Table 5.…”

Section: Resultsmentioning

confidence: 99%

“…We illustrate this method by calculating the heat of vaporization and solubility parameter of ethylchloride using a generic force field, the Dreiding force field, 16 and quantum mechanically determined electrostatic potential atomic charges [C(Ϫ0.049)H 3 (0.0424)C(Ϫ0.077)H 2 (0.1079)Cl(Ϫ0.217) numbers in parenthesis are in electron charge units]. For simplicity we start the simulation using the experimental liquid density (0.9 g/cc), a requirement that becomes unnecessary in the method described as the Cohesive Energy Density (CED) protocol below.…”

Section: Npt Molecular Dynamics Methodsmentioning

confidence: 99%

“…4. The force field parameters are taken from a suitable force field, such as the generic Dreiding force field, 16 Universal force field (UFF 18 ) etc. 5.…”

Section: Ced Methodsmentioning

confidence: 99%

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Hildebrand and Hansen solubility parameters from Molecular Dynamics with applications to electronic nose polymer sensors

et al. 2004

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Abstract:We introduce the Cohesive Energy Density (CED) method, a multiple sampling Molecular Dynamics computer simulation procedure that may offer higher consistency in the estimation of Hildebrand and Hansen solubility parameters. The use of a multiple sampling technique, combined with a simple but consistent molecular force field and quantum mechanically determined atomic charges, allows for the precise determination of solubility parameters in a systematic way ( ϭ 0.4 hildebrands). The CED method yields first-principles Hildebrand parameter predictions in good agreement with experiment [root-mean-square (rms) ϭ 1.1 hildebrands]. We apply the CED method to model the Caltech electronic nose, an array of 20 polymer sensors. Sensors are built with conducting leads connected through thin-film polymers loaded with carbon black. Odorant detection relies on a change in electric resistivity of the polymer film as function of the amount of swelling caused by the odorant compound. The amount of swelling depends upon the chemical composition of the polymer and the odorant molecule. The pattern is unique, and unambiguously identifies the compound. Experimentally determined changes in relative resistivity of seven polymer sensors upon exposure to 24 solvent vapors were modeled with the CED estimated Hansen solubility components. Predictions of polymer sensor responses result in Pearson R 2 coefficients between 0.82 and 0.99.

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Section: Resultsmentioning

confidence: 99%

Section: Npt Molecular Dynamics Methodsmentioning

confidence: 99%

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Hildebrand and Hansen solubility parameters from Molecular Dynamics with applications to electronic nose polymer sensors

et al. 2004

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“…This category includes AMBER [56,57,58], COMPASS [59], OPLS-AA [60] and CHARMM [61]; (b) generic potentials such as DREIDING [62] and UFF [63] that are not parameterized to reproduce properties of any particular set of molecules but based on simple hybridization considerations; (c) specialized force fields that are parameterized to reproduce properties of a specific compound that cannot be properly represented by existing force field sets.…”

Section: Force Fieldmentioning

confidence: 99%

Effect of Cross-Linking on the Diffusion of Water, Ions, and Small Molecules in Hydrogels

2009

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Understanding the diffusion of small molecules in hydrogel system is of major importance in a variety of applications including drug delivery systems, tissue engineering and contact lens. Cross-linking density of hydrogels has been commonly used to tune key parameters like mesh size and molecular weight between cross-linkers, in order to change macroscopic properties of hydrogels. In this thesis, molecular dynamics investigations of chemically-cross-linked poly(ethylene glycol) (PEG) hydrogels are reported with the aim of exploring the diffusion properties of water, ions, and rhodamine within the polymer at the molecular level.The water structure and diffusion properties were studied at various cross-linking densities with molecular weights of the chains ranging from 572 to 3400. As the cross-linking density is increased, the water diffusion decreases and the slowdown in diffusion is more severe at the polymer-water interface. The water diffusion at various cross-linking densities is correlated with the water hydrogen bonding dynamics. The diffusion of ions and rhodamine also decreased as the cross-linking density is increased. The variation of diffusion coefficient with cross-linking density is related to the variation of water content at different cross-linking densities.Comparison of simulation results and obstruction scaling theory for hydrogels showed similar trends.ii To Father and Mother.iii

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“…Each edge has a weight which is linearly related to the bond energy. The bond strengths are obtained from the DRIEDING force-field 40 . This protein graph is encoded by a weighted adjacency matrix A, an N × N symmetric matrix (where N is the number of atoms in the protein) in which the entry A i j gives the energy of the interaction between atoms i and j (0 if there is no interaction 26 , and is thus well suited for the analysis of the protein graph at all scales.…”

Section: Construction Of the Atomistic Networkmentioning

confidence: 99%

Uncovering allosteric pathways in caspase-1 using Markov transient analysis and multiscale community detection

et al. 2014

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Allosteric regulation at distant sites is central to many cellular processes. In particular, allosteric sites in proteins are a major target to increase the range and selectivity of new drugs, and there is a need for methods capable of identifying intra-molecular signalling pathways leading to allosteric effects. Here, we use an atomistic graph-theoretical approach that exploits Markov transients to extract such pathways and exemplify our results in an important allosteric protein, caspase-1. Firstly, we use Markov Stability community detection to perform a multiscale analysis of the structure of caspase-1 which reveals that the active conformation has a weaker, less compartmentalised large-scale structure as compared to the inactive conformation, resulting in greater intra-protein coherence and signal propagation. We also carry out a full computational point mutagenesis and identify that only a few residues are critical to such structural coherence. Secondly, we characterise explicitly the transients of random walks originating at the active site and predict the location of a known allosteric site in this protein quantifying the contribution of individual bonds to the communication pathway between the active and allosteric sites. Several of the bonds we find have been shown experimentally to be functionally critical, but we also predict a number of as yet unidentified bonds which may contribute to the pathway. Our approach offers a computationally inexpensive method for the identification of allosteric sites and communication pathways in proteins using a fully atomistic description.

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DREIDING: a generic force field for molecular simulations

Cited by 5,761 publications

References 0 publications

Hildebrand and Hansen solubility parameters from Molecular Dynamics with applications to electronic nose polymer sensors

Hildebrand and Hansen solubility parameters from Molecular Dynamics with applications to electronic nose polymer sensors

Effect of Cross-Linking on the Diffusion of Water, Ions, and Small Molecules in Hydrogels

Uncovering allosteric pathways in caspase-1 using Markov transient analysis and multiscale community detection

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