Molecular dynamics (MD) is a computer simulation method for analyzing the physical motion of atoms and molecules. In order to comprehend the dynamical "evolution" of the system, it permits atoms and molecules to interact with one another for a predetermined amount of time. The technique involves the use of numerical integration of Newton's equations of motion to generate atomic trajectories of the system in order to obtain specific interatomic potentials and boundary conditions defined by initial conditions. It is widely acknowledged that computer simulations of macromolecules using classical mechanics principles to describe atomic behavior are important. In order to advance research in mechanics, energy, and complex biological systems using cutting-edge MD simulation techniques, Alfa Chemistry provides MD simulation services.
Fig 1. The MD-generated atomic pattern for 2,4,5-trinitrobenzoic acid. (Raggi G, et al. 2020)
Our MD Simulation Services Include
In molecular dynamics, a molecule is described as a series of charged points (atoms) connected by springs (bonds). Force fields have been applied to explain the temporal evolution of bond lengths, bond angles, and torsion as well as non-bonded van der Waals forces and electrostatic interactions between atoms. A set of equations and related constants known as a force field is intended to replicate particular aspects of the molecular geometry and test structure. The simplicity of the force field representation of molecular features: springs of bond lengths and angles, periodic functions of bond rotations and Lennard-Jones potentials, and Coulomb's law for van der Waals and electrostatic interactions, respectively, ensure that energy and force calculations are very fast even for large systems. Our scientists offer a variety of force field methods, including AMBER, OPLS, and GROMOS, to perform molecular dynamics simulations of individual systems.
We can use molecular mechanics simulations to provide molecular energy as a function of stretching, bending, twisting, etc. This is an approximate model. Our capabilities include binding energy, decomposition energy, and thermodynamic Gibbs free energy.
The dynamic behavior of stable macromolecules at limited temperatures has been extensively studied using molecular dynamics simulations. The majority of conformational transformations, however, either happen by chance in simulations or at extraordinarily high temperatures outside the normal range of experimental settings. By using time-dependent, purely geometric constraints, targeted molecular dynamics (TMD) is a technique for generating conformational changes in known target structures at ambient temperature. One possible application of TMD is the search for energetic barriers and stable intermediates ranging from fairly localized changes to protein denaturation.
|Project Name||Molecular Dynamics Simulation Service|
|Deliverables||We provide all raw data and analysis services to our customers.|
|Samples Requirement||Our services require specific requirements from you.|
|Timeline Decide||According to customers' needs|
|Price||Please contact us for an inquiry|
- Our high performance computing systems can quickly complete a huge number of calculations.
- Our computer specialists are adept at using the top MD simulation programs and software codes.
- We can employ MD simulations in a range of applications thanks to our expertise and wealth of experience.
- Our services are affordable and efficient at advancing different studies.
Alfa Chemistry provides fast, professional, high-quality MD simulation services at competitive prices to clients worldwide. We need to evaluate each project before determining the appropriate analysis plan and pricing. If you are interested in our services, please contact us for more details.
- Polanski J, et al. (2009). "Chemoinformatics." Comprehensive Chemometrics. Chemical and Biochemical Data Analysis: 459-506.