Molecular dynamics simulations with constrained roto-translational motions: Theoretical basis and statistical mechanical consistency

Amadei, Andrea; Chillemi, Giovanni; Ceruso, Marc A.; Grottesi, Alessandro; Nola, Alfredo Di

doi:10.1063/1.480557

Cited by 101 publications

(122 citation statements)

References 11 publications

Supporting

Mentioning

122

Contrasting

Order By: Relevance

“…The trajectories were then propagated for 20 ns in a NVT ensemble using an integration step of 2.0 fs with the rototranslational constrain (25) applied to the solute. It is worth noting that these simulations are, at least to our knowledge, the longest ever performed on such system.…”

Section: Accepted M Manuscriptmentioning

confidence: 99%

The role of Arginine 38 in horseradish peroxidase enzyme revisited: A computational investigation

Tatoli¹,

Zazza²,

Sanna³

et al. 2009

Biophysical Chemistry

View full text Add to dashboard Cite

Section: Accepted M Manuscriptmentioning

confidence: 99%

The role of Arginine 38 in horseradish peroxidase enzyme revisited: A computational investigation

Tatoli¹,

Zazza²,

Sanna³

et al. 2009

Biophysical Chemistry

View full text Add to dashboard Cite

“…Temperature has been controlled by the Berendsen's coupling algorithm with a time constant equal to the time step to approximate the Gaussian isokinetic thermostat. 41,42 Long-range electrostatic interactions have been calculated using the particle-mesh Ewald method and applying a cutoff of 0.9 nm to the short-range Lennard-Jones interactions. The SETTLE algorithm 43 is used to fix the water molecule geometry, and the SHAKE algorithm, 44 to constrain the O-H distance in the PVA hydroxylic groups.…”

Section: Simulation Detailsmentioning

confidence: 99%

Supercooled Water in PVA Matrixes. II. A Molecular Dynamics Simulation Study and Comparison with QENS Results

2005

View full text Add to dashboard Cite

Molecular dynamics (MD) simulations were carried out to elucidate the dynamic behavior of water confined in poly(vinyl alcohol), PVA, hydrogels. Model topology is supported by experimental network parameters, and simulation results are compared to an incoherent quasielastic neutron scattering (QENS) investigation carried out on PVA hydrogels.1 From the QENS dynamic scattering law (part I), 1 a random jump model was adopted for the description of water diffusion to extract a microscopic diffusion coefficient and a residence time between two "jumps". In the present work, consistently with this framework, water diffusion parameters as diffusion coefficients and residence times have been evaluated using the mean square displacement of water in a time window of 10 ps and the time autocorrelation function of water hydrogen bonds. The calculated parameters are in good agreement with the experimental ones, giving confidence to this approach. Further developments are in progress to take into account a more realistic description of hydrogel structure in the molecular dynamics simulations.

show abstract

“…Mathematical proof has been given that rotational degrees of freedom can be removed without affecting the statistical mechanical ensemble, 3 and it has been demonstrated that the use of an NDLP unit cell in conjunction with rotational constraints does not lead to detectable changes relative to simulations performed in a rhombic dodecahedron.…”

Section: ■ Introductionmentioning

confidence: 99%

SQUEEZE-E: The Optimal Solution for Molecular Simulations with Periodic Boundary Conditions

Wassenaar

Vries

Bonvin

et al. 2012

J. Chem. Theory Comput.

View full text Add to dashboard Cite

In molecular simulations of macromolecules, it is desirable to limit the amount of solvent in the system to avoid spending computational resources on uninteresting solvent−solvent interactions. As a consequence, periodic boundary conditions are commonly used, with a simulation box chosen as small as possible, for a given minimal distance between images. Here, we describe how such a simulation cell can be set up for ensembles, taking into account a priori available or estimable information regarding conformational flexibility. Doing so ensures that any conformation present in the input ensemble will satisfy the distance criterion during the simulation. This helps avoid periodicity artifacts due to conformational changes. The method introduces three new approaches in computational geometry: (1) The first is the derivation of an optimal packing of ensembles, for which the mathematical framework is described. (2) A new method for approximating the α-hull and the contact body for single bodies and ensembles is presented, which is orders of magnitude faster than existing routines, allowing the calculation of packings of large ensembles and/or large bodies. 3. A routine is described for searching a combination of three vectors on a discretized contact body forming a reduced base for a lattice with minimal cell volume. The new algorithms reduce the time required to calculate packings of single bodies from minutes or hours to seconds. The use and efficacy of the method is demonstrated for ensembles obtained from NMR, MD simulations, and elastic network modeling. An implementation of the method has been made available online at http://haddock.chem.uu.nl/services/SQUEEZE/ and has been made available as an option for running simulations through the weNMR GRID MD server at

show abstract

Molecular dynamics simulations with constrained roto-translational motions: Theoretical basis and statistical mechanical consistency

Cited by 101 publications

References 11 publications

The role of Arginine 38 in horseradish peroxidase enzyme revisited: A computational investigation

The role of Arginine 38 in horseradish peroxidase enzyme revisited: A computational investigation

Supercooled Water in PVA Matrixes. II. A Molecular Dynamics Simulation Study and Comparison with QENS Results

SQUEEZE-E: The Optimal Solution for Molecular Simulations with Periodic Boundary Conditions

Contact Info

Product

Resources

About