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Molecular dynamics simulation of highly charged proteins: comparison of the particle-particle particle-mesh and reaction field methods for the calculation of electrostatic interactions.

ABSTRACT: Molecular dynamics (MD) simulations of the activation domain of porcine procarboxypeptidase B (ADBp) were performed to examine the effect of using the particle-particle particle-mesh (P3M) or the reaction field (RF) method for calculating electrostatic interactions in simulations of highly charged proteins. Several structural, thermodynamic, and dynamic observables were derived from the MD trajectories, including estimated entropies and solvation free energies and essential dynamics (ED). The P3M method leads to slightly higher atomic positional fluctuations and deviations from the crystallographic structure, along with somewhat lower values of the total energy and solvation free energy. However, the ED analysis of the system leads to nearly identical results for both simulations. Because of the strong similarity between the results, both methods appear well suited for the simulation of highly charged globular proteins in explicit solvent. However, the lower computational demand of the RF method in the present implementation represents a clear advantage over the P3M method.

SUBMITTER: Gargallo R

PROVIDER: S-EPMC2366931 | biostudies-literature | 2003 Oct

REPOSITORIES: biostudies-literature

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Molecular dynamics simulation of highly charged proteins: comparison of the particle-particle particle-mesh and reaction field methods for the calculation of electrostatic interactions.

Gargallo Raimundo R Hünenberger Philippe H PH Avilés Francesc X FX Oliva Baldomero B

Protein science : a publication of the Protein Society 20031001 10

Molecular dynamics (MD) simulations of the activation domain of porcine procarboxypeptidase B (ADBp) were performed to examine the effect of using the particle-particle particle-mesh (P3M) or the reaction field (RF) method for calculating electrostatic interactions in simulations of highly charged proteins. Several structural, thermodynamic, and dynamic observables were derived from the MD trajectories, including estimated entropies and solvation free energies and essential dynamics (ED). The P3 ...[more]

PMID: 14500874

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Project description:In electron optics, calculation of the electric field plays a major role in all computations and simulations. Accurate field calculation methods such as the finite element method (FEM), boundary element method and finite difference method, have been used for years. However, such methods are computationally very expensive and make the computer simulation challenging or even infeasible when trying to apply automated design of electrostatic lens systems with many free parameters. Hence, for years, electron optics scientists have been searching for a fast and accurate method of field calculation to tackle the aforementioned problem in the design and optimization of electrostatic electron lens systems. This paper presents a novel method for fast electric field calculation in electrostatic electron lens systems with reasonably high accuracy to enable the electron-optical designers to design and optimize an electrostatic lens system with many free parameters in a reasonably short time. The essence of the method is to express the off-axis potential in an axially symmetrical coordinate system in terms of derivatives of the axial potential up to the fourth order, and equate this to the potential of the electrode at that axial position. Doing this for a limited number of axial positions, we get a set of equations that can be solved to obtain the axial potential, necessary for calculating the lens properties. We name this method the fourth-order electrode method because we take the axial derivatives up to the fourth order. To solve the equations, a quintic spline approximation of the axial potential is calculated by solving three sets of linear equations simultaneously. The sets of equations are extracted from the Laplace equation and the fundamental equations that describe a quintic spline. The accuracy and speed of this method is compared with other field calculation methods, such as the FEM and second order electrode method (SOEM). The new field calculation method is implemented in design/optimization of electrostatic lens systems by using a genetic algorithm based optimization program for electrostatic lens systems developed by the authors. The effectiveness of this new field calculation method in optimizing optical parameters of electrostatic lens systems is compared with FEM and SOEM and the results are presented. It should be noted that the formulation is derived for general axis symmetrical electrostatic electron lens systems, however the examples shown in this paper are with cylindrical electrodes due to the simplicity of the implementation in the software.

Project description:BackgroundAmong other causes the long-term result of hip prostheses in dogs is determined by aseptic loosening. A prevention of prosthesis complications can be achieved by an optimization of the tribological system which finally results in improved implant duration. In this context a computerized model for the calculation of hip joint loadings during different motions would be of benefit. In a first step in the development of such an inverse dynamic multi-body simulation (MBS-) model we here present the setup of a canine hind limb model applicable for the calculation of ground reaction forces.MethodsThe anatomical geometries of the MBS-model have been established using computer tomography- (CT-) and magnetic resonance imaging- (MRI-) data. The CT-data were collected from the pelvis, femora, tibiae and pads of a mixed-breed adult dog. Geometric information about 22 muscles of the pelvic extremity of 4 mixed-breed adult dogs was determined using MRI. Kinematic and kinetic data obtained by motion analysis of a clinically healthy dog during a gait cycle (1 m/s) on an instrumented treadmill were used to drive the model in the multi-body simulation.Results and discussionAs a result the vertical ground reaction forces (z-direction) calculated by the MBS-system show a maximum deviation of 1.75%BW for the left and 4.65%BW for the right hind limb from the treadmill measurements. The calculated peak ground reaction forces in z- and y-direction were found to be comparable to the treadmill measurements, whereas the curve characteristics of the forces in y-direction were not in complete alignment.ConclusionIn conclusion, it could be demonstrated that the developed MBS-model is suitable for simulating ground reaction forces of dogs during walking. In forthcoming investigations the model will be developed further for the calculation of forces and moments acting on the hip joint during different movements, which can be of help in context with the in silico development and testing of hip prostheses.

Dataset Information

Molecular dynamics simulation of highly charged proteins: comparison of the particle-particle particle-mesh and reaction field methods for the calculation of electrostatic interactions.

Publications

Molecular dynamics simulation of highly charged proteins: comparison of the particle-particle particle-mesh and reaction field methods for the calculation of electrostatic interactions.

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