LINCS: A linear constraint solver for molecular simulations

Hess, Berk; Bekker, Henk; Berendsen, Herman J. C.; Fraaije, J. G. E. M.

doi:10.1002/(sici)1096-987x(199709)18:12<1463::aid-jcc4>3.0.co;2-h

Cited by 13,521 publications

(5,521 citation statements)

References 10 publications

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“…For each system, a short (100 ps) MD run was then carried out using a 1 fs integration step, followed by a full 200 ns or 400 ns run (for pure POPC or POPC/cholesterol bilayers, respectively) using a 2 fs integration step. Bond lengths were constrained to their equilibrium values, using the SETTLE algorithm [43] for water and the LINCS algorithm [44] for all other bonds. All simulations were carried out under constant number of particles, pressure (1 bar) and temperature (300 K), and with periodic boundary conditions.…”

Section: Methodsmentioning

confidence: 99%

Diphenylhexatriene membrane probes DPH and TMA-DPH: A comparative molecular dynamics simulation study

Canto

Robalo

Santos

et al. 2016

Biochimica et Biophysica Acta (BBA) - Biomembranes

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Fluorescence spectroscopy and microscopy have been utilized as tools in membrane biophysics for decades now. Because phospholipids are non-fluorescent, the use of extrinsic membrane probes in this context is commonplace. Among the latter, 1,6-diphenylhexatriene (DPH) and its trimethylammonium derivative (TMA-DPH) have been extensively used. It is widely believed that, owing to its additional charged group, TMA-DPH is anchored at the lipid/water interface and reports on a bilayer region that is distinct from that of the hydrophobic DPH. In this study, we employ atomistic MD simulations to characterize the behavior of DPH and TMA-DPH in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and POPC/cholesterol (4:1) bilayers. We show that although the dynamics of TMA-DPH in these membranes is noticeably more hindered than that of DPH, the location of the average fluorophore of TMA-DPH is only~3-4 Å more shallow than that of DPH. The hindrance observed in the translational and rotational motions of TMA-DPH compared to DPH is mainly not due to significant differences in depth, but to the favorable electrostatic interactions of the former with electronegative lipid atoms instead. By revealing detailed insights on the behavior of these two probes, our results are useful both in the interpretation of past work and in the planning of future experiments using them as membrane reporters.

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Section: Methodsmentioning

confidence: 99%

Diphenylhexatriene membrane probes DPH and TMA-DPH: A comparative molecular dynamics simulation study

Canto

Robalo

Santos

et al. 2016

Biochimica et Biophysica Acta (BBA) - Biomembranes

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“…The Simple Point Charge (SPC/E) water model 31 was used with the 43A1-S3 force field and the SPC water model 32 was used with other force fields. The SET-TLE algorithm 33 was used to constrain water molecules and the Linear Constraint Solver (LINCS) 34 was used to constrain all other bond lengths in the system. In general, simulation parameters for non-bonded interactions were chosen to be the same as those used by the workers who created the force fields.…”

Section: B Simulation Parametersmentioning

confidence: 99%

Effects of truncating van der Waals interactions in lipid bilayer simulations

Huang

Garcı́a

2014

The Journal of Chemical Physics

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In membrane simulations, it is known that truncating electrostatic interactions results in artificial ordering of lipids at the truncation distance. However, less attention has been paid to the effect of truncating van der Waals (VDW) interactions. Since the VDW potential decays as r −6 , it is frequently neglected beyond a cutoff of around 1 nm. In some cases, analytical dispersion corrections appropriate for isotropic systems are applied to the pressure and the potential energy. In this work, we systematically study the effect of truncating VDW interactions at different cutoffs in 1,2-Dipalmitoylsn-glycero-3-phosphocholine bilayers with the Berger force field. We show that the area per lipid decreases systematically when the VDW cutoff (r c ) increases. This dependence persists even when dispersion corrections are applied. Since the analytical form of the dispersion correction is only appropriate for isotropic systems, we suggest that a long VDW cutoff should be used in preference over a short VDW cutoff. To determine the appropriate cutoff, we simulate liquid pentadecane with the Berger parameters and find that r c ≥ 1.4 nm is sufficient to reproduce the density and the heat of vaporization of pentadecane. Bilayers simulated with r c ≥ 1.4 nm show an improved agreement with experiments in both the form factors and the deuterium order parameters. Finally, we report that the VDW cutoff has a significant impact on the lipid flip-flop energetics and an inappropriate short VDW cutoff results in a bilayer that is prone to form water defects across the bilayer. © 2014 AIP Publishing LLC. [http://dx

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“…The time step was set at 2 fs. The bonds involving hydrogen atoms in the protein were constrained according to the LINCS 76 algorithm. Explicit solvent simulations were performed using TIP3P model 77 of water.…”

Section: Computational Detailsmentioning

confidence: 99%

Reduced atomic pair-interaction design (RAPID) model for simulations of proteins

Baumketner

2013

The Journal of Chemical Physics

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Increasingly, theoretical studies of proteins focus on large systems. This trend demands the development of computational models that are fast, to overcome the growing complexity, and accurate, to capture the physically relevant features. To address this demand, we introduce a protein model that uses all-atom architecture to ensure the highest level of chemical detail while employing effective pair potentials to represent the effect of solvent to achieve the maximum speed. The effective potentials are derived for amino acid residues based on the condition that the solvent-free model matches the relevant pair-distribution functions observed in explicit solvent simulations. As a test, the model is applied to alanine polypeptides. For the chain with 10 amino acid residues, the model is found to reproduce properly the native state and its population. Small discrepancies are observed for other folding properties and can be attributed to the approximations inherent in the model. The transferability of the generated effective potentials is investigated in simulations of a longer peptide with 25 residues. A minimal set of potentials is identified that leads to qualitatively correct results in comparison with the explicit solvent simulations. Further tests, conducted for multiple peptide chains, show that the transferable model correctly reproduces the experimentally observed tendency of polyalanines to aggregate into β-sheets more strongly with the growing length of the peptide chain. Taken together, the reported results suggest that the proposed model could be used to succesfully simulate folding and aggregation of small peptides in atomic detail. Further tests are needed to assess the strengths and limitations of the model more thoroughly.

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LINCS: A linear constraint solver for molecular simulations

Cited by 13,521 publications

References 10 publications

Diphenylhexatriene membrane probes DPH and TMA-DPH: A comparative molecular dynamics simulation study

Diphenylhexatriene membrane probes DPH and TMA-DPH: A comparative molecular dynamics simulation study

Effects of truncating van der Waals interactions in lipid bilayer simulations

Reduced atomic pair-interaction design (RAPID) model for simulations of proteins

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