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Molecular Dynamics (GROMACS) — Free Certification Assessment

StemSkills Lab > Molecular Dynamics (GROMACS) — Free Certification Assessment

Molecular Dynamics (GROMACS) — Free Certification Assessment

Test your knowledge of MD and GROMACS — ensembles, force fields, PME, RMSD/RMSF, equilibration. Pass at 70% to earn a verifiable StemSkills certificate you can download as a PDF and add to your LinkedIn profile. Free.

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Molecular Dynamics (GROMACS) — Certification Assessment

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Free certification assessment. Pass at 70% to earn a verifiable StemSkills certificate.

  • Questions count: 20
  • Passing grade: 70%
  • Time limit: 20 minutes
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1.
Molecular dynamics simulates atomic motion by numerically integrating:
The heat equation only
Schrödinger's equation for all electrons
Newton's equations of motion under a force field
The Michaelis–Menten equation
2.
In GROMACS, the tool that prepares a run input (.tpr) by combining structure, topology, and parameters is:
gmx solvate
gmx rms
gmx trjconv
gmx grompp
3.
A GROMACS force field provides:
The crystallographic R-factor
The camera angle for rendering
Bonded and non-bonded parameters (bonds, angles, LJ, charges)
The sequence alignment score
4.
Periodic boundary conditions (PBC) are used to:
Freeze the protein
Increase the timestep to 1 ns
Remove all water
Mimic bulk solvent and avoid surface/edge artifacts
5.
A typical MD integration timestep for all-atom simulations (with constrained H-bonds) is about:
2 milliseconds
2 seconds
2 femtoseconds
2 minutes
6.
The NVT ensemble holds constant:
Number, Volume, Temperature
Volume and enthalpy
Number, Pressure, Temperature
Energy only
7.
The NPT ensemble is typically used to equilibrate:
The force field version
Temperature only
System density via constant pressure (and temperature)
The sequence
8.
RMSD of the protein backbone over a trajectory primarily measures:
Overall structural deviation from a reference over time
The number of hydrogen bonds
Per-residue flexibility
The solvent viscosity
9.
RMSF (root-mean-square fluctuation) is most useful for:
Identifying flexible vs rigid regions per residue
Global drift
Measuring pressure
Counting atoms
10.
A thermostat (e.g., V-rescale, Nosé–Hoover) is used to:
Add ligands
Align two proteins
Compute RMSD
Control/maintain the system temperature
11.
A barostat (e.g., Parrinello–Rahman) controls:
Bond length
Temperature
Pressure (by scaling the box)
Charge
12.
Energy minimization before MD is performed to:
Remove bad contacts/steric clashes before dynamics
Delete the water
Randomize velocities
Heat the system to 500 K
13.
In GROMACS, `gmx solvate` is used to:
Generate the topology
Add ions only
Fill the simulation box with solvent (water)
Compute the RMSD
14.
Adding ions with `gmx genion` typically serves to:
Remove hydrogens
Align sequences
Neutralize net charge and/or set physiological salt concentration
Increase temperature
15.
The PME (Particle Mesh Ewald) method handles:
Long-range electrostatic interactions efficiently
Temperature coupling
Bond constraints
Trajectory conversion
16.
LINCS/SETTLE algorithms are used to:
Compute free energy
Add solvent
Constrain bond lengths (allowing a larger timestep)
Increase the box size
17.
`gmx trjconv` is commonly used to:
Add ions
Build a topology
Post-process trajectories (e.g., fix PBC, extract frames, center)
Run minimization
18.
Which indicates a reasonably equilibrated simulation?
An empty water box
RMSF of exactly zero
Stable temperature, pressure, energy, and plateaued RMSD
Continuously rising temperature
19.
The radius of gyration (Rg) of a protein reports on its:
Force field
Number of chains
Net charge
Compactness / overall size
20.
A production MD run differs from equilibration mainly in that it:
Always uses vacuum
Uses no force field
Collects data for analysis under the target ensemble after equilibration
Removes the protein
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