This section is dealing with specific types of analysis performed by MDANSE. If you are not sure where these fit into the general workflow of data analysis, please read MDANSE Workflow.

Analysis: Other๏ƒ

This section contains background theory for following plugins:

Infrared๏ƒ

Infrared๏ƒ

Calculates the molecular infrared spectrum averaged over all molecules in the trajectory. The infrared spectrum is calculated from the Fourier transform of the autocorrelation of the time-derivative of the molecular dipole:

(134)๏ƒ\[I(\omega) \propto \frac{1}{N_{m}}\sum_{m} \frac{1}{6\pi} \int \mathrm{d}t \, \left\langle \dot{\vec{\mu}}_{m}(0) \cdot \dot{\vec{\mu}}_{m}(t) \right\rangle e^{-i\omega t}\]

where \(N_{m}\) is the number of molecules and \(\dot{\vec{\mu}}_{m}(t)\) is the time-derivative of the molecular dipole moment of molecule \(m\).

Dipole Autocorrelation Function๏ƒ

Calculates the molecular dipole autocorrelation function which is closely related to the molecular infrared spectrum

(135)๏ƒ\[\mathrm{DACF}(t) = \frac{1}{3 N_{m}}\sum_{m} \left\langle \vec{\mu}_{m}(0) \cdot \vec{\mu}_{m}(t) \right\rangle\]

where \(N_{m}\) is the number of molecules \(m\) and \(\vec{\mu}(t)\) is the molecular dipole moment of molecule \(m\).

Thermodynamics๏ƒ

Density๏ƒ

Density is used in molecular dynamics simulations to calculate and analyze the density of particles within a simulated system. Density refers to the concentration of particles (atoms, molecules, or ions) in a given volume of space. This helps researchers understand how particles are distributed within the simulation box and how their density changes over time. By calculating density profiles or histograms, scientists can gain insights into phase transitions, the formation of clusters, or the behavior of molecules in various regions of the system. Understanding density is crucial for studying phase changes, solvation, and other thermodynamic processes in molecular systems.

Temperature๏ƒ

The temperature is another essential tool in molecular dynamics simulations that allows researchers to monitor and control the temperature of the simulated system. Temperature is a fundamental thermodynamic variable that influences molecular motion and interactions. This plugin provides the means to calculate and adjust the temperature throughout a simulation, ensuring that the system remains at the desired temperature or follows a specific temperature profile. Monitoring temperature fluctuations and deviations from the desired values is crucial for accurately simulating and understanding the thermodynamic behavior of molecules. Controlling temperature is particularly important when studying phase transitions, chemical reactions, and equilibrium properties of molecular systems.

Trajectory๏ƒ

Center Of Masses Trajectory๏ƒ

The center of mass trajectory (COMT) analysis consists in deriving the trajectory of the respective centres of mass of a set of groups of atoms. In order to produce a visualizable trajectory, MDANSE assigns the centres of mass to pseudo-hydrogen atoms whose mass is equal to the mass of their associated group. Thus, the produced trajectory can be reused for other analysis. In that sense, COMT analysis is a practical way to reduce noticeably the dimensionality of a system.

Trajectory Editor๏ƒ

It is a general-purpose tool for writing out a new trajectory with contents different to the input one.

At the moment, the main applications include:

  • molecule detection,

  • setting unit cell parameters,

  • setting partial charges,

  • removing or transmuting atoms,

  • removing frames.