MagiC: Software Package for Multiscale Modeling

Mirzoev, Alexander; Lyubartsev, Alexander P.

doi:10.1021/ct301019v

Cited by 61 publications

(75 citation statements)

References 57 publications

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“…Table 1. Parameters of the coarse-grained (CG) DNA model developed from the inverse Monte Carlo analysis [62] using data of all atom molecular dynamic (MD) simulations. Force constants were derived from potential functions approximated by harmonic potential.…”

Section: Design Of the Flexible Cg Dna Model And Principles Of Its Pamentioning

confidence: 99%

“…The counterions were also included into CG trajectory. The CG trajectory generated from the atomistic simulations was used to extract effective coarse-grained potentials by the inverse Monte Carlo method [19,62]. For that, radial distribution functions between the sites of the CG model, as well as internal bond and angle distributions between the CG sites were determined from the CG trajectory and were used as input to the inverse Monte Carlo procedure.…”

Section: Coarse-grained Dna and Computations Of Effective Potentialsmentioning

confidence: 99%

“…As a result of the inverse Monte Carlo computations, effective pair potentials between all CG sites, and internal bond and angle potentials were determined which reproduce the RDFs, as well as bond and angle distributions of the atomistic model. The computations were carried out using the software package MagiC [62].…”

Section: Coarse-grained Dna and Computations Of Effective Potentialsmentioning

confidence: 99%

“…Figure 1B). RDFs were calculated from the data of all-atom MD simulations; potential functions were determined using inverse Monte Carlo method [62]. In calculations of RDFs and potentials 22-bp DNA fragment was coarse-grained on two types ("D" and "P") particles and particles in the middle of the DNA were treated separately from the particles at the DNA ends.…”

Section: Harmonic Approximation For Internal Potentialsmentioning

confidence: 99%

“…The parameterization is based on atomistic simulations of DNA oligomers in water solution with K + as counterions. The internal coarse-grained DNA potentials are then computed by the inverse Monte Carlo method using the MagiC software [62] to reproduce the internal DNA structure and dynamics obtained in atomistic simulations. The Inverse Monte Carlo method with this software has been shown to be robust and rigorous [63] and is implemented with 2-body interactions as well as 3-body angular potentials and the inclusion of these interactions can be done straightforwardly and with high efficiency in computational effort.…”

Section: Introductionmentioning

confidence: 99%

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A Coarse-Grained DNA Model Parameterized from Atomistic Simulations by Inverse Monte Carlo

et al. 2014

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Abstract:Computer modeling of very large biomolecular systems, such as long DNA polyelectrolytes or protein-DNA complex-like chromatin cannot reach all-atom resolution in a foreseeable future and this necessitates the development of coarse-grained (CG) approximations. DNA is both highly charged and mechanically rigid semi-flexible polymer and adequate DNA modeling requires a correct description of both its structural stiffness and salt-dependent electrostatic forces. Here, we present a novel CG model of DNA that approximates the DNA polymer as a chain of 5-bead units. Each unit represents two DNA base pairs with one central bead for bases and pentose moieties and four others for phosphate groups. Charges, intra-and inter-molecular force field potentials for the CG DNA model were calculated using the inverse Monte Carlo method from all atom molecular dynamic (MD) simulations of 22 bp DNA oligonucleotides. The CG model was tested by performing dielectric continuum Langevin MD simulations of a 200 bp double helix DNA in solutions of monovalent salt with explicit ions. Excellent agreement with experimental data was obtained for the dependence of the DNA persistent length on salt concentration in the range 0.1-100 mM. The new CG DNA model is suitable for modeling various biomolecular systems with adequate description of electrostatic and mechanical properties.

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Section: Design Of the Flexible Cg Dna Model And Principles Of Its Pamentioning

confidence: 99%

Section: Coarse-grained Dna and Computations Of Effective Potentialsmentioning

confidence: 99%

Section: Coarse-grained Dna and Computations Of Effective Potentialsmentioning

confidence: 99%

Section: Harmonic Approximation For Internal Potentialsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A Coarse-Grained DNA Model Parameterized from Atomistic Simulations by Inverse Monte Carlo

et al. 2014

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Predicting the Self‐Assembly of Superparamagnetic Colloids under Magnetic Fields

Faraudo

Andreu

Calero

et al. 2016

Adv Funct Materials

107

114

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Self‐assembly processes are very important in material sciences but are particularly difficult to predict quantitatively. This is the case for particulate magnetic materials in which field‐induced self‐assembly processes are essential. This article describes the recent advances in the development of predictive theoretical tools for the study of directed self‐assembly of superparamagnetic colloids under magnetic fields. A practical view is presented of how to employ the new concepts (derived from thermodynamic theory) to predict the possible assembled structures from the properties of the colloids and thermodynamic conditions. Quantitative prediction of kinetics is also discussed for the cases in which equilibrium theory is not relevant. Finally, an outline of fundamental aspects of the theory is presented.

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Systematic implicit solvent coarse graining of dimyristoylphosphatidylcholine lipids

Mirzoev

Lyubartsev

2014

J Comput Chem

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We have used systematic structure-based coarse graining to derive effective site-site potentials for a 10-site coarse-grained dimyristoylphosphatidylcholine (DMPC) lipid model and investigated their state point dependence. The potentials provide for the coarse-grained model the same site-site radial distribution functions, bond and angle distributions as those computed in atomistic simulations carried out at four different lipid-water molar ratios. It was shown that there is a non-negligible dependence of the effective potentials on the concentration at which they were generated, which is also manifested in the properties of the lipid bilayers simulated using these potentials. Thus, effective potentials computed at low lipid concentration favor to more condensed and ordered structure of the bilayer with lower average area per lipid, while potentials obtained at higher lipid concentrations provide more fluid-like structure. The best agreement with the reference data and experiment was achieved using the set of potentials derived from atomistic simulations at 1:30 lipid:water molar ratio providing fully saturated hydration of DMPC lipids. Despite theoretical limitations of pairwise coarse-grained potentials expressed in their state point dependence, all the resulting potentials provide a stable bilayer structure with correct partitioning of different lipid groups across the bilayer as well as acceptable values of the average lipid area, compressibility and orientational ordering. In addition to bilayer simulations, the model has proven its robustness in modeling of self-aggregation of lipids from randomly dispersed solution to ordered bilayer structures, bicelles, and vesicles.

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MagiC: Software Package for Multiscale Modeling

Cited by 61 publications

References 57 publications

A Coarse-Grained DNA Model Parameterized from Atomistic Simulations by Inverse Monte Carlo

A Coarse-Grained DNA Model Parameterized from Atomistic Simulations by Inverse Monte Carlo

Predicting the Self‐Assembly of Superparamagnetic Colloids under Magnetic Fields

Systematic implicit solvent coarse graining of dimyristoylphosphatidylcholine lipids

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