MCP 1 Chapter 3 Molecular Dynamics

Questions about the lecture 'From Molecular to Continuum Physics 1' of the RWTH Aachen Chapter 3 Molecular Dynamics

Questions about the lecture 'From Molecular to Continuum Physics 1' of the RWTH Aachen Chapter 3 Molecular Dynamics

126

0.0 (0)

R. B.

Study

R. B.

About these flashcards

This flashcard set delves into advanced molecular dynamics (MD) techniques at the university level, focusing on key concepts like NPT and NVT ensembles, pressure and temperature control methods, and their implementation in tools like GROMACS. It covers essential topics such as the Parrinello-Rahman and Berendsen algorithms, their characteristics, and activation procedures. Researchers and students in computational chemistry and molecular physics will find this set particularly useful for understanding and applying these methods in their simulations.

Flashcards

126

Students

1

Language

English

Category

Computer Science

Level

University

Created / Updated

18.02.2017 / 21.02.2017

What to use in case of pairwise interactions via potential phi(r) for P?

[isothermal-isobaric NPT ensembles.MD]

P = rho*k_b*T – 1/Vd * < Sum_i=1^N Sum_j>i r_ij dphi/dr >

What is the virial theorem?

[isothermal-isobaric NPT ensembles.MD, 2]

1. Link conecpt of mac pressure and mic dynamics

2. PV = N*k_B*T + 1/3 * < Sum_i=1^N r_i*f_i >

What is the idea?

[time evolution algorithm.isothermal-isobaric NPT ensembles.MD]

Coordinate scaling with ad hoc modulation of coordinates

What are the characteristics?

[berendsen.time evolution algorithm.isothermal-isobaric NPT ensembles.MD, 4]

1. Mimics pressure coupling with first-order kinetics relaxation with pressure towards P^ref

2. Rescale each particle’s coordinates and box vectors

3. Correct system pressure

4. Repeat periodically

How to rescale?

[berendsen.time evolution algorithm.isothermal-isobaric NPT ensembles.MD, 3]

1. Use time-dependent matrix

2. mye_ij = d_ij – n*dt/tao_p *b_ij {P_ij^Ref – P_ij(t)}

3. With b_ij the isothermal compressibility

How to correct system pressure?

[berendsen.time evolution algorithm.isothermal-isobaric NPT ensembles.MD]

dP/dt = P^ref-P/tao_p

How to active in GROMACS?

[berendsen.time evolution algorithm.isothermal-isobaric NPT ensembles.MD, 5]

1. pcoupl = berendsen

2. pcoupltype = isotropic

3. ref-p = 0.79

4. tau-p = 0.5

5. compressibility = 2e-4

What are the effects?

[berendsen.time evolution algorithm.isothermal-isobaric NPT ensembles.MD, 2]

1. Yields correct average pressure

2. Not yield exact isobaric ensemble

What is the idea?

[equations of motions.isothermal-isobaric NPT ensembles.MD]

Extended ensemble with new variables added to 6N phase space

Which methods exist?

[equations of motions.isothermal-isobaric NPT ensembles.MD, 3]

1. Andersen

2. Parrinello-Rahman

3. MTTK

What are the characteristics?

[parrinello-rahman.equations of motions.isothermal-isobaric NPT ensembles.MD, 5]

1. Extended by new DoF and terms

2. DoF represent box vectors represented by matrix h

3. h obeys equation of motion

4. Equation of motions changes

5. Micocanonical sampling yields isobaric distribution

How does h obeys the equation of motion?

[parrinello-rahman.equations of motions.isothermal-isobaric NPT ensembles.MD, 2]

1. d²h/dt² = VW^-1(h^T)^-1(P-P^ref)

2. With (W^-1)_ij = 4pi²*b_ij / 3tao_p*max(h_ij)

How does the equation of motion changes?

[parrinello-rahman.equations of motions.isothermal-isobaric NPT ensembles.MD, 2]

1. d²r_i/dt² = f_i/m_i – M dr_i/dt

2. With M = h^-1[h dh^T/dt + dh/dt h^T](h^T)^-1

How to active in GROMACS?

[parrinello-rahman.equations of motions.isothermal-isobaric NPT ensembles.MD, 5]

1. pcoupl = parrinello-rahman

2. pcoupltype = isotropic

3. ref-p = 0.79

4. tau-p = 0.5

5. compressibility = 2e-4

What are the effects?

[parrinello-rahman.equations of motions.isothermal-isobaric NPT ensembles.MD, 2]

1. Yields true ensemble

2. Not reversible due to usage of old pressure // Missing high precision

What are the steps?

[equilibration procedure.isothermal-isobaric NPT ensembles.MD, 2]

1. Initial heating

2. Employ barostat algorithm to find correct density

How to react if pressure far from equilibrium?

[equilibration procedure.isothermal-isobaric NPT ensembles.MD, 3]

1. Increase time constant

2. OR use weak-coupling scheme

3. After target pressure reached switch back

What to do?

[temperature and pressure.equilibration procedure.isothermal-isobaric NPT ensembles.MD, 3]

1. Use same type of algorithm

2. Berendsen thermostat + Berendsen barostat

3. Nose-Hoover thermostat + Parrinello-Rahman barostat

What are the characteristics?

[berendsen.temperature and pressure.equilibration procedure.isothermal-isobaric NPT ensembles.MD, 2]

1. Weak coupling

2. Does not yield exact NPT ensemble

What are the characteristics?

[nose-hoover parrinello-rahman.temperature and pressure.equilibration procedure.isothermal-isobaric NPT ensembles.MD, 2]

1. Extended ensemble approach

2. Yields exact NPT ensemble

What are the characteristics of experiments in the past? [3]

Keyboard commands:

= turn,

= for-/backward,

= scroll

1. System subjected to measurements

2. Results in numeric form compared with...

3. Theory is a model of the system as a set of mathematical equations

What are the characteristics of experiments nowadays using computers? [5]

Keyboard commands:

= turn,

= for-/backward,

= scroll

1. Following a recipe

2. More complexity

3. Large amount of degrees of freedom

4. Simulation condition close to experimental one

5. Thought experiments possible

What is the definition of molecular dynamics (MD)? [4]

Keyboard commands:

= turn,

= for-/backward,

= scroll

1. Computer simulation of a set of atoms time evolution due to motion

2. Numerically integration of motion equations with time discretization Dt

3. N material points move deterministically

4. m_i* d²r_1/dt² = f_i wuth r_i position vector and f_i force vector

What are the limitations of molecular dynamics (MD)? [4]

Keyboard commands:

= turn,

= for-/backward,

= scroll

1. Accuracy improved by increased numerical precision or smaller Dt

2. Classical laws of motion

3. Realism of forces // Force-filed problem

4. Time and size

What can be done with molecular dynamics (MD)?

Keyboard commands:

= turn,

= for-/backward,

= scroll

Measure thermodynamic properties

What are the components of a physical system model? [2]

Keyboard commands:

= turn,

= for-/backward,

= scroll

1. Potential function U(r_1,… ,r_n) representing potential energy

2. Forces f_i are gradients of the potential -Grad_r_i(U)

What are the notes for a physical system model? [3]

Keyboard commands:

= turn,

= for-/backward,

= scroll

1. Conservation law o the total energy E=K+U

2. For simulated system N is negligible small compared to amount in matter

3. Use PBC to mimic as replicating a small box (program) in all directions

What is the definition of the Lennard-Jones pair potential for the potential function? [3]

Keyboard commands:

= turn,

= for-/backward,

= scroll

1. Interaction Sum_i Sum_j>i phi(|r_i-r_j|)

2. phi(r) = 4*eps*[(sigma/r)^12 – [sigma/r]^6]

3. Describes correctly e.g. for liquid Argon

What is a practical extension of the Lennard-Jones pair potential for the potential function? [3]

Keyboard commands:

= turn,

= for-/backward,

= scroll

1. Short-range interaction potential saves resources

2. Lennard-Jones has infinite range

3. Cutoff radius is practical with R_c=3sigma

What has to be done if the short-range interaction potential is applied to the Lennard-Jones pair potential for the potential function? [4]

Keyboard commands:

= turn,

= for-/backward,

= scroll

1. Constant additive correction for quantities

2. Treat system as a uniform continuum beyond cutoff

3. phi_ij^LRC = ½*4pi*p*int_Rc^inf(dr_ij*r_ij²*phi(r_ij)) = 8pi*p*eps*sigma³*[1/9(sigma/Rc)^9 – 1/3(sigma/Rc)^3]

4. P_ij^LRC = = ½*4pi*p²*int_Rc^inf(dr_ij*r_ij²*r_ij*F_ij) = 16/3*pi*p²*eps*sigma³*[2/3(sigma/Rc)^9 – (sigma/Rc)^3] with p=N/V the number density

What is the meaning of the abbreviation GROMACS?

Groningen machine for chemical simulations

What is GROMACS for?

Molecular dynamics package for simulations of proteins, lipids and nucleic acids

What are the characteristics of GROMACS? [3]

1. Used at universities and research centers across the world

2. Fast and most popular MD SW available

3. Open source

Which file type exist in GROMACS? [3]

1. Topology 2. coordinate and 3. simulation parameter

What is the question answered by a topology file in GROMACS?

How Is the system to be run? // Force-filed parameters

What is the question answered by a coordinate file in GROMACS?

Where is the system to be run? // Coordinates of atoms

What is the question answered by a simulation parameter file in GROMACS?

What do you want to run? // Time step and cutoffs

How to indicate comments in a topology file in GROMACS?

With a semicolon ;

What are the categories of a topology file in GROMACS? [6]

1. [defaults]

2. [atomtypes]

3. [moleculetype]

4. [atoms]

5. [system]

6. [molecules]

What are the sub categories of [defaults] of a topology file in GROMACS? [2]

1. nb-function

2. combination rule

1 / 126

Flashcards

What are the effects?

[parrinello-rahman.equations of motions.isothermal-isobaric NPT ensembles.MD, 2]

1. Yields true ensemble

2. Not reversible due to usage of old pressure // Missing high precision

What are the steps?

[equilibration procedure.isothermal-isobaric NPT ensembles.MD, 2]

1. Initial heating

2. Employ barostat algorithm to find correct density

How to react if pressure far from equilibrium?

[equilibration procedure.isothermal-isobaric NPT ensembles.MD, 3]

1. Increase time constant

2. OR use weak-coupling scheme

3. After target pressure reached switch back

What to do?

[temperature and pressure.equilibration procedure.isothermal-isobaric NPT ensembles.MD, 3]

1. Use same type of algorithm

2. Berendsen thermostat + Berendsen barostat

3. Nose-Hoover thermostat + Parrinello-Rahman barostat

What are the characteristics?

[berendsen.temperature and pressure.equilibration procedure.isothermal-isobaric NPT ensembles.MD, 2]

1. Weak coupling

2. Does not yield exact NPT ensemble

What are the characteristics?

[nose-hoover parrinello-rahman.temperature and pressure.equilibration procedure.isothermal-isobaric NPT ensembles.MD, 2]

1. Extended ensemble approach

2. Yields exact NPT ensemble

1
2
3
4

Study