1,721,439 research outputs found
Ensemble of transition state structures for the cis-trans isomerization of N-methylacetamide
No full textThe cis-trans isomerization of N-methylacetamide (NMA), a model peptidic fragment, is studied theoretically in vacuo and in explicit water solvent at 300 K using the metadynamics technique. The computed cis-trans free energy difference is very similar for NMA(g) and NMA(aq), in agreement with experimental measurements of population ratios and theoretical studies at 0 K. By exploiting the flexibility in the definition of a pair of recently introduced collective variables (Branduardi, D.; Gervasio, F. L.; Parrinello, M. J. Chem. Phys. 2007, 126, 054103), an ensemble of transition state structures is generated at finite temperature for both NMA(g) and NMA(aq), as verified by computing committor distribution functions. Ensemble members of NMA(g) are shown to have correlated values of the backbone dihedral angle and a second dihedral angle involving the amide hydrogen atom. The dynamical character of these structures is preserved in the presence of solvent, whose influence on the committor functions can be modeled using effective friction/noise terms
Accurate sampling using Langevin dynamics
No full textWe show how to derive a simple integrator for the Langevin equation and illustrate how it is possible to check the accuracy of the obtained distribution on the fly, using the concept of effective energy introduced in a recent paper [J. Chem. Phys. 126, 014101 (2007)]. Our integrator leads to correct sampling also in the difficult high-friction limit. We also show how these ideas can be applied in practical simulations, using a Lennard-Jones crystal as a paradigmatic case
Stochastic thermostats: comparison of local and global schemes
No full textWe show that a recently introduced stochastic thermostat [J. Chem. Phys. 126 (2007) 014101] can be considered as a global version of the Langevin thermostat. We compare the global scheme and the local one (Langevin) from a formal point of view and through practical calculations on a model Lennard-Jones liquid. At variance with the local scheme, the global thermostat preserves the dynamical properties for a wide range of coupling parameters, and allows for a faster sampling of the phase-space
Accurate Quantum Chemical Free Energies at Affordable Cost
No full textFree energy sampling methods allow studying the full dynamics of activated processes. Unfortunately, the affordable accuracy of the potential describing the energy and forces of the system is usually rather low. Here we introduce a new method that by combining metadynamics and free energy perturbation allows calculating accurate quantum chemical free energies for chemical reactions. To prove the effectiveness of this new approach we study the SN2 reaction of CH3F + Cl- → CH3Cl + F- in vacuo and solvated by water. Comparisons are made with harmonic transition-state theory to show how this method could provide accurate equilibrium and rate constants for complex systems
Water molecule dipole in the gas and in the liquid phase.
No full textWe study with ab initio molecular dynamics the change that the electric dipole moment of water molecules undergoes in passing from the gas to the liquid phase. Our analysis is based on the recently introduced maximally localized Wannier functions and is devoid of the ambiguities that have affected previous attempts. We find that in the liquid the dipole moment has an average value of about 3 D, 60% higher than in the gas phase. This value is much larger than is currently assumed (2.6 D). Furthermore, a broad distribution around this average value is observed. The relevance of these results for current modeling of water is discussed
Using Metadynamics to Understand the Mechanism of Calmodulin/Target Recognition at Atomic Detail
No full textAbstractThe ability of calcium-bound calmodulin (CaM) to recognize most of its target peptides is caused by its binding to two hydrophobic residues (‘anchors’). In most of the CaM complexes, the anchors pack against the hydrophobic pockets of the CaM domains and are surrounded by fully conserved Met side chains. Here, by using metadynamics simulations, we investigate quantitatively the energetics of the final step of this process using the M13 peptide, which has a high affinity and spans the sequence of the skeletal myosin light chain kinase, an important natural CaM target. We established the accuracy of our calculations by a comparison between calculated and NMR-derived structural and dynamical properties. Our calculations provide novel insights into the mechanism of protein/peptide recognition: we show that the process is associated with a free energy gain similar to that experimentally measured for the CaM complex with the homologous smooth muscle MLCK peptide (Ehrhardt et al., 1995, Biochemistry 34, 2731). We suggest that binding is dominated by the entropic effect, in agreement with previous proposals. Furthermore, we explain the role of conserved methionines by showing that the large flexibility of these side chains is a key feature of the binding mechanism. Finally, we provide a rationale for the experimental observation that in all CaM complexes the C-terminal domain seems to be hierarchically more important in establishing the interaction
Conjugate gradient heat bath for ill-conditioned actions.
No full textWe present a method for performing sampling from a Boltzmann distribution of an ill-conditioned quadratic action. This method is based on heat-bath thermalization along a set of conjugate directions, generated via a conjugate-gradient procedure. The resulting scheme outperforms local updates for matrices with very high condition number, since it avoids the slowing down of modes with lower eigenvalue, and has some advantages over the global heat-bath approach, compared to which it is more stable and allows for more freedom in devising case-specific optimizations
Nuclear quantum effects in solids using a colored-noise thermostat.
No full textWe present a method, based on a non-Markovian Langevin equation, to include quantum corrections to the classical dynamics of ions in a quasiharmonic system. By properly fitting the correlation function of the noise, one can vary the fluctuations in positions and momenta as a function of the vibrational frequency, and fit them so as to reproduce the quantum-mechanical behavior, with minimal a priori knowledge of the details of the system. We discuss the application of the thermostat to diamond and to ice Ih. We find that results in agreement with path-integral methods can be obtained using only a fraction of the computational effort
Ab initio molecular dynamics simulation of laser melting of graphite.
No full textThe method of ab initio molecular dynamics, based on finite temperature density functional theory, is used to simulate laser heating of graphite. We find that a sufficiently high concentration of excited electrons dramatically weakens the covalent bond. As a result the system undergoes an ultrafast melting transition to a metallic state. This process appears to be similar to, although considerably faster than, laser melting of silicon. The properties of the laser-induced liquid phase of carbon are found to depend crucially on the level of electronic excitation. All these features are in qualitative agreement with the experimental behavior
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