Effects of bundling on the properties of the SPC water model

Fuhrmans, Marc; Sanders, Barbara P.; Marrink, Siewert J.; Vries, Alex H. de

doi:10.1007/s00214-009-0590-4

Cited by 85 publications

(135 citation statements)

References 26 publications

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“…To facilitate the supramolecular (in the present case 4-to-1) coupling, where multiple molecules are mapped always to the same CG bead, we need to restrict the relative motion of these molecules; this means that the molecules cannot diffuse far away from each other, thus ensuring a meaningful correspondence between AT and CG coordinates. Accordingly we model the water in the high resolution region with the bundled-SPC [24,25] water model, where an attractive semi-harmonic potential is added between all oxygen atoms within a bundle. In addition, the oxygen-oxygen Lennard-Jones interaction is modified to match the density of the SPC water.…”

Section: Multiscale Modelmentioning

confidence: 99%

“…We use parameters that correspond to model 1 in Ref. [24], which outperforms the alternative bundled-SPC model 2 [26]. For the ions we employ the GROMOS [39] and MARTINI [14] force fields in the AT and CG regions, respectively.…”

Section: Multiscale Modelmentioning

confidence: 99%

“…The bundled-SPC water model has somewhat different properties compared to the original SPC water model [24,26]. To assess the changes induced by the bundling, we replot (Fig.…”

Section: Effect Of Bundlingmentioning

confidence: 99%

“…To perform efficient mapping between the AT and supramolecular CG water models, we made use of AT bundled-SPC water models, where the molecules mapped to the same CG bead are restrained by distance-dependent potentials [24,25]. The introduction of additional constraints to some extent alters the properties of the model compared to the unrestrained model.…”

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confidence: 99%

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Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution

Zavadlav

Podgornik

Melo

et al. 2016

Eur. Phys. J. Spec. Top.

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Abstract. We present a dual-resolution model of a deoxyribonucleic acid (DNA) molecule in a bathing solution, where we concurrently couple atomistic bundled water and ions with the coarse-grained MAR-TINI model of the solvent. We use our fine-grained salt solution model as a solvent in the inner shell surrounding the DNA molecule, whereas the solvent in the outer shell is modeled by the coarse-grained model. The solvent entities can exchange between the two domains and adapt their resolution accordingly. We critically asses the performance of our multiscale model in adaptive resolution simulations of an infinitely long DNA molecule, focusing on the structural characteristics of the solvent around DNA. Our analysis shows that the adaptive resolution scheme does not produce any noticeable artifacts in comparison to a reference system simulated in full detail. The effect of using a bundled-SPC model, required for multiscaling, compared to the standard free SPC model is also evaluated. Our multiscale approach opens the way for large scale applications of DNA and other biomolecules which require a large solvent reservoir to avoid boundary effects.

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Section: Multiscale Modelmentioning

confidence: 99%

Section: Multiscale Modelmentioning

confidence: 99%

“…The bundled-SPC water model has somewhat different properties compared to the original SPC water model [24,26]. To assess the changes induced by the bundling, we replot (Fig.…”

Section: Effect Of Bundlingmentioning

confidence: 99%

mentioning

confidence: 99%

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Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution

Zavadlav

Podgornik

Melo

et al. 2016

Eur. Phys. J. Spec. Top.

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“…As a proof of principle, we simulated a 56-residue protein G, at full atomistic detail, solvated in water molecules that dynamically change resolution between an atomistic representation -a bundled version 33 of the Simple Point Charge (SPC) model 34 -and a mesoscopic one -the MARTINI CG model. 35,36 The successful interfacing with the widely used MARTINI CG model opens up a range of future applications involving the broad variety of solutes and solvents parameterized for this force field.…”

mentioning

confidence: 99%

Adaptive resolution simulation of an atomistic protein in MARTINI water

Zavadlav

Melo

Marrink

et al. 2014

The Journal of Chemical Physics

109

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We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coarse-grained model via a 4-to-1 molecule coarse-grain mapping by using bundled water models, i.e., we restrict the relative movement of water molecules that are mapped to the same coarse-grained bead employing harmonic springs. The water molecules change their resolution from four molecules to one coarse-grained particle and vice versa adaptively on-the-fly. Having performed 15 ns long molecular dynamics simulations, we observe within our error bars no differences between structural (e.g., root-mean-squared deviation and fluctuations of backbone atoms, radius of gyration, the stability of native contacts and secondary structure, and the solvent accessible surface area) and dynamical properties of the protein in the adaptive resolution approach compared to the fully atomistically solvated model. Our multiscale model is compatible with the widely used MARTINI force field and will therefore significantly enhance the scope of biomolecular simulations.

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Reconstruction of atomistic details from coarse‐grained structures

et al. 2010

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We present an algorithm to reconstruct atomistic structures from their corresponding coarse-grained (CG) representations and its implementation into the freely available molecular dynamics (MD) program package GROMACS. The central part of the algorithm is a simulated annealing MD simulation in which the CG and atomistic structures are coupled via restraints. A number of examples demonstrate the application of the reconstruction procedure to obtain low-energy atomistic structural ensembles from their CG counterparts. We reconstructed individual molecules in vacuo (NCQ tripeptide, dipalmitoylphosphatidylcholine, and cholesterol), bulk water, and a WALP transmembrane peptide embedded in a solvated lipid bilayer. The first examples serve to optimize the parameters for the reconstruction procedure, whereas the latter examples illustrate the applicability to condensed-phase biomolecular systems.

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Effects of bundling on the properties of the SPC water model

Cited by 85 publications

References 26 publications

Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution

Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution

Adaptive resolution simulation of an atomistic protein in MARTINI water

Reconstruction of atomistic details from coarse‐grained structures

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