molecular dynamics simulation

USAGE SUMMARY

The phrase "molecular dynamics simulation" is correct and usable in written English.
You can use it to refer to a computer simulation of the behavior of a system of molecules, typically used to study and predict chemical reactions. For example, "The scientist used a molecular dynamics simulation to predict the outcome of the reaction."

✓ Grammatically correct

Science

Human-verified examples from authoritative sources

Exact Expressions

60 human-written examples

Each orientation was subjected to simulated annealing molecular dynamics simulation.

Acta Pharmaceutica Sinica B

Extended Data Fig. 10 Dynamic hydrogen-bond network within the NTH domain observed by molecular dynamics simulation.

Nature

Molecular Dynamics Simulation of Chaperone-mediated Protein Folding.

Stanford University

Shibuta, Y. & Maruyama, S. Molecular dynamics simulation of generation process of SWNTs.

Nature

Pang, J. & Allemann, R. K. Molecular dynamics simulation of thermal unfolding of Thermatoga maritima DHFR.

Nature

Molecular dynamics simulation to rationalize regioselective hydroxylation of aromatic substrates by soluble methane monooxygenase.

Nature

Feller, S. E., Zhang, Y., Pastor, R. W. & Brooks, B. R. Constant pressure molecular dynamics simulation: the Langevin piston method.

Nature

Dong, X. et al. Homology modeling and molecular dynamics simulation of the HIF2α degradation-related HIF2α-VHL complex.

Nature

Extended Data Fig. 9 Analysis of K+ trajectories and putative binding site observed during molecular dynamics simulation.

Nature

Kitchen, D. B., Reed, L. H. & Levy, R. M. Molecular dynamics simulation of solvated protein at high pressure.

Nature

These guys have carried out a molecular dynamics simulation to study how such a process might work.

MIT Technology Review

Expert writing Tips

Best practice

When writing about "molecular dynamics simulation", specify the software or method used (e.g., GROMACS, NAMD, or umbrella sampling) for clarity and reproducibility.

Common error

Avoid using "molecular dynamics simulation" interchangeably with other methods like Monte Carlo simulations or energy minimization. MD simulates the time-dependent behavior of molecules, while other methods may have different goals.

Linguistic Context

The phrase "molecular dynamics simulation" functions as a noun phrase, typically used as a subject or object in a sentence. As Ludwig AI confirms, it refers to a computational method and is commonly used in scientific writing.

Expression frequency: Very common

Frequent in

Science

100%

Less common in

News & Media

0%

Formal & Business

0%

Academia

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Ludwig's WRAP-UP

The phrase "molecular dynamics simulation" is a grammatically correct and widely used noun phrase, primarily in scientific contexts to denote a computational method for studying molecular behavior. Ludwig AI confirms its validity and common usage. Key related phrases include "MD simulation" and "molecular dynamics modeling". When using the phrase, specify the methods and software for clarity. Avoid confusing it with other simulation techniques. The frequency of the phrase is very common in scientific literature.

More alternative expressions

Phrases that express similar concepts, ordered by semantic similarity:

MD simulation

This is a shortened, commonly used abbreviation for "molecular dynamics simulation".

Molecular dynamics modeling

Replaces "simulation" with "modeling", implying a similar computational process with a focus on model creation.

Computational molecular dynamics

Adds "computational" to emphasize the computational aspect of the simulation.

All-atom molecular dynamics

Specifies that the simulation considers all atoms in the system, providing a higher level of detail.

Coarse-grained molecular dynamics

Indicates a simulation using a simplified representation of the molecules to reduce computational cost.

Molecular simulation

A broader term that encompasses various simulation methods, including molecular dynamics.

Atomistic simulation

Highlights the atomic-level detail of the simulation, focusing on individual atoms and their interactions.

Classical molecular dynamics

Indicates that the simulation uses classical mechanics to describe the motion of atoms.

Enhanced sampling molecular dynamics

Describes techniques used to overcome barriers in simulations, allowing for better exploration of phase space.

In silico molecular dynamics

Adds "in silico" to emphasize that the simulation is performed on a computer.

FAQs

How is "molecular dynamics simulation" used in scientific research?

Researchers use "molecular dynamics simulation" to study the physical movements of atoms and molecules. It's employed in understanding protein folding, drug binding, material properties and a wide range of other phenomena.

What are some alternatives to "molecular dynamics simulation"?

Depending on the context, you might use terms like "MD simulation" (a common abbreviation), "molecular dynamics modeling", or simply "molecular simulation".

What is the difference between "molecular dynamics simulation" and "Monte Carlo simulation"?

"Molecular dynamics simulation" evolves a system over time using equations of motion, whereas "Monte Carlo simulation" uses random sampling to explore possible states without explicitly simulating dynamics. Each method has its strengths depending on the research question.

What kind of data can be obtained from a "molecular dynamics simulation"?

A "molecular dynamics simulation" can provide information on the positions and velocities of atoms over time, allowing calculation of properties like energy, pressure, diffusion coefficients and structural changes. It's a powerful tool for studying molecular behavior.