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
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Lernkarten
What are the characteristics of experiments in the past? [3]
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]
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]
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]
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)?
Measure thermodynamic properties
What are the components of a physical system model? [2]
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]
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]
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]
1. Short-range interaction potential saves resources
2. Lennard-Jones has infinite range
3. Cutoff radius is practical with Rc=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]
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
What are the choices for the nb-functions in [defaults] of a topology file in GROMACS? [2]
1 is Lennard-Jones
2 is Buckingham
What are the choices for the combination rule in [defaults] of a topology file in GROMACS? [2]
1 and 3 with
- C_ij^e = sqrt(C_i^e*C_j^e) with e\in{6,12}
- C_i^e = 4*eps_i*s_i^e
2 is s_ij = ½*(s_i+s_j) and eps_ij = sqrt(eps_i*eps_j)
What are the sub categories of [atomtypes] of a topology file in GROMACS? [7]
1. name
2. number
3. mass [u]
4. charge [e]
5. ptype
6. sigma [nm]
7. epsilon [kJ/mol]
What are the choices for the ptype in [atomtypes] of a topology file in GROMACS? [3]
1. A for atom
2. S for shell // polarizable force fields
3. V or D for virtual atom
What are the sub categories of [moleculetype] of a topology file in GROMACS? [2]
1. name
2. nrexcl // How to deal with non-bonded interactions
What are the sub categories of [atoms] of a topology file in GROMACS? [6]
1. Nr
2. Type // Information from [atomtypes] section
3. Resnr
4. Residue // Information for identification in pdb file
5. Atom // Information for identification in pdb file
6. Cgnr // Charge group number
What is the sub category of [system] of a topology file in GROMACS?
Name
What are the sub categories of [molecules] of a topology file in GROMACS? [2]
1. Compound
2. # mols
How can we create coordination files with python scripts in GROMACS?
./script_name.py -l cubic -o coordinates.pdb 512
Name to formats for coordinate files in GROMACS? [2]
1. XYZ and 2. PDB
How does the XYZ format for coordinate files in GROMACS looks like? [4]
N
[Comment]
atom1 x y z …
atomN x y z
How does the PDB format for coordinate files in GROMACS looks like? [5]
[Title]
[Comment]
ATOM 1 Ar Ar A 1 x y z 1.00 0.00 …
ATOM N Ar Ar A N x y z 1.00 0.00
END
What is the definition for column number 3 in the PDB format for coordinate files in GROMACS?
Atom name defined in topology file
What is the definition for column number 4 in the PDB format for coordinate files in GROMACS?
Residue name defined in topology file
What is the definition for column number 5 in the PDB format for coordinate files in GROMACS?
Chain identifier
What is the definition for column number 6 in the PDB format for coordinate files in GROMACS?
Residue number
What is the definition for column number 10 in the PDB format for coordinate files in GROMACS?
Occupancy factor
What is the definition for column number 11 in the PDB format for coordinate files in GROMACS?
Temperature factor
What is VMD for?
Molecular visualization program for analyzing biomolecular systems
What are the characteristics of VMD? [2]
1. Can read standard PDB files with vmd file_name.pdb
2. Open source
