Category:Advanced molecular-dynamics sampling: Difference between revisions

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In a molecular-dynamics (MD) calculation, we are often interested in rare events or specific transitions. Advanced molecular-dynamics sampling helps to capture these during an MD run within a feasible simulation time.

Theory

Constrained molecular dynamics

In constrained molecular dynamics selected geometric parameters are constrained during the calculations. This is achieved by extending the Lagrangian with a term incorporating the desired constraints (SHAKE^[1] algorithm) directly. This method can be used on its own to support molecular dynamics calculations but some of the methods on this page also incorporate constraints via the same methodology.

Constrained molecular dynamics.

Biased molecular dynamics

Biased molecular dynamics refers to methods introducing a bias potential. In one of this method's most popular representatives, the umbrella sampling or umbrella integration, the bias potential is used to pin the system to given configurations. This way the the sampling of a system is greatly enhanced and thermodynamic methods with proper statistics become accessible. Although some of the methods on this page also use bias potentials they have differences in the usage of the potential and hence belong in their categories.

Biased molecular dynamics are often used to calculate free energies or free energy differences.

Biased molecular dynamics.

Interface pinning

In interface pinning two different phases of the same system are simulated in a single simulation box. The goal of this method is to look for the right conditions where both phases would coexist, which corresponds to a phase transition point. Above a transition point, the whole system would quickly turn into one phase and below the point into the other phase. With this, the transition point could be searched via bi-sectioning, but this would involve a huge effort. To accelerate the search for a phase transition point the order parameters are used to control the composition of the box and the force that would drive the system towards equilibrium is used to estimate the phase transition point.

Interface pinning is usually used to determine melting points (solid-liquid interface).

Interface pinning.

Metadynamics

In metadynamics, a bias potential that acts on a few selected geometric parameters (collective variables) is added to the Hamiltonian of a system. The bias potential is constantly built up during a molecular dynamics run by adding Gaussian hills at selected time increments. This way even deep potential minima can be filled and overcome.

This method is good for exploring new phases of a given system.

Metadynamics.

Blue moon ensemble

The blue moon ensemble method is designed to calculate the free energy profile along the path of selected reaction coordinates. It also employs constraining of the atoms during molecular dynamics (SHAKE^[1] algorithm). The term "blue moon" refers to rare events such as the "moon turning blue".

The method is often used to calculate free energy differences for systems where the profile is characterized by a few barriers that are high enough that they would not be crossed within regular thermostatted molecular dynamics.

Blue moon ensemble.

Slow-growth approach

In the slow-growth approach, the free energy profile is scanned along a reaction coordinate. The scanning is done by linearly changing the reaction coordinate from that of the reactant state to that of a transition or product state via constrained molecular dynamics (SHAKE^[1] algorithm).

Like in the blue moon ensemble, this method is also designed to calculate free energy differences for systems where the profile is characterized by a few barriers that are high enough that they would not be crossed within regular thermostatted molecular dynamics.

Slow-growth approach.

Thermodynamic integration

In the thermodynamic integration method, the energy differences of a fully interacting and non-interacting system are calculated. This is achieved by making the potential energy depend on a coupling parameter and defining the free energy as a smooth integral over the potential energy along this coupling parameter. As the reference state for a non-interacting system usually an ideal gas or a harmonic solid is chosen.

Thermodynamic integration is usually used to compute free energy differences between different phases.

Thermodynamic integration

How to

References

↑ ^a ^b ^c J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comp. Phys. 23, 327 (1977).

Subcategories

This category has the following 2 subcategories, out of 2 total.

B

Biased molecular dynamics

T

Transition states

Pages in category "Advanced molecular-dynamics sampling"

The following 41 pages are in this category, out of 41 total.

[ryckaertt:jcp:1977-1] J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comp. Phys. 23, 327 (1977).

[1]

@@ Line 1: / Line 1: @@
-In a [[:Category:Molecular dynamics|molecular-dynamics]](MD) calculation, we are often interested in rare events or specific transitions. '''Advanced molecular-dynamics sampling''' helps to capture these during an MD run within the reasonable simulation.
+In a [[:Category:Molecular dynamics|molecular-dynamics]] (MD) calculation, we are often interested in rare events or specific transitions. '''Advanced molecular-dynamics sampling''' helps to capture these during an MD run within a feasible simulation time.
 == Theory ==
-*Interface pinning: {{TAG|Interface pinning calculations}}.
-*Constrained molecular dynamics: {{TAG|Constrained molecular dynamics}}.
+=== Constrained molecular dynamics ===
-*Metadynamics: {{TAG|Metadynamics}}.
+In constrained molecular dynamics selected geometric parameters are constrained during the calculations. This is achieved by extending the Lagrangian with a term incorporating the desired constraints (SHAKE{{cite|ryckaertt:jcp:1977}} algorithm) directly.                                                                                                                                                                                                             This method can be used on its own to support molecular dynamics calculations but some of the methods on this page also incorporate constraints via the same methodology.
-*Biased molecular dynamics: {{TAG|Biased molecular dynamics}}.
+*[[Constrained molecular dynamics]].
-*Slow-growth approach: {{TAG|Slow-growth approach}}.
+=== Biased molecular dynamics ===
+Biased molecular dynamics refers to methods introducing a bias potential. In one of this method's most popular representatives, the umbrella sampling or umbrella integration, the bias potential is used to pin the system to given configurations. This way the the sampling of a system is greatly enhanced and thermodynamic methods with proper statistics become accessible. Although some of the methods on this page also use bias potentials they have differences in the usage of the potential and hence belong in their categories.
+Biased molecular dynamics are often used to calculate free energies or free energy differences.
+*{{TAG|Biased molecular dynamics}}.
+=== Interface pinning ===
+In interface pinning two different phases of the same system are simulated in a single simulation box. The goal of this method is to look for the right conditions where both phases would coexist, which corresponds to a phase transition point. Above a transition point, the whole system would quickly turn into one phase and below the point into the other phase. With this, the transition point could be searched via bi-sectioning, but this would involve a huge effort. To accelerate the search for a phase transition point the order parameters are used to control the composition of the box and the force that would drive the system towards equilibrium is used to estimate the phase transition point.
+Interface pinning is usually used to determine melting points (solid-liquid interface).
+*[[Interface pinning]].
+=== Metadynamics ===
+In metadynamics, a bias potential that acts on a few selected geometric parameters (collective variables) is added to the Hamiltonian of a system. The bias potential is constantly built up during a molecular dynamics run by adding Gaussian hills at selected time increments. This way even deep potential minima can be filled and overcome.
+This method is good for exploring new phases of a given system.
+*[[Metadynamics]].
+=== Blue moon ensemble ===
+The blue moon ensemble method is designed to calculate the free energy profile along the path of selected reaction coordinates. It also employs constraining of the atoms during molecular dynamics (SHAKE{{cite|ryckaertt:jcp:1977}} algorithm). The term "blue moon" refers to rare events such as the "moon turning blue".
+The method is often used to calculate free energy differences for systems where the profile is characterized by a few barriers that are high enough that they would not be crossed within regular thermostatted molecular dynamics.
+*{{TAG|Blue moon ensemble}}.
+=== Slow-growth approach ===
+In the slow-growth approach, the free energy profile is scanned along a reaction coordinate. The scanning is done by linearly changing the reaction coordinate from that of the reactant state to that of a transition or product state via constrained molecular dynamics (SHAKE{{cite|ryckaertt:jcp:1977}} algorithm).
+Like in the blue moon ensemble, this method is also designed to calculate free energy differences for systems where the profile is characterized by a few barriers that are high enough that they would not be crossed within regular thermostatted molecular dynamics.
+*{{TAG|Slow-growth approach}}.
+=== Thermodynamic integration ===
+In the thermodynamic integration method, the energy differences of a fully interacting and non-interacting system are calculated. This is achieved by making the potential energy depend on a coupling parameter and defining the free energy as a smooth integral over the potential energy along this coupling parameter. As the reference state for a non-interacting system usually an ideal gas or a harmonic solid is chosen.
+Thermodynamic integration is usually used to compute free energy differences between different phases.
+*[[Thermodynamic integration]]
 == How to ==
-*Interface pinning: {{TAG|Interface pinning calculations}}.
+*[[Constrained molecuar dynamics calculations]].
-*Constrained molecular dynamics: {{TAG|Constrained molecular dynamics}}.
+*[[Biased molecular dynamics calculations]]
-*Metadynamics: {{TAG|Metadynamics}}.
+*[[Interface pinning calculations]].
-*Biased molecular dynamics: {{TAG|Biased molecular dynamics}}.
+*[[Metadynamics calculations]].
-*Slow-growth approach: {{TAG|Slow-growth approach}}.
+*[[Blue moon ensemble calculations]].
-*Thermodynamic integration: [[:Category:Thermodynamic integration|Thermodynamic integration]]
+*[[Slow-growth approach calculations]].
+*[[Thermodynamic integration calculations]].
 == References ==
 [[Category:VASP|Advanced molecular-dynamics sampling]][[Category:Molecular dynamics|Molecular dynamics]]