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Free Molecular Dynamics (GROMACS) Certification Assessment

Test your knowledge of molecular dynamics with GROMACS: ensembles, force fields, PME, RMSD and RMSF, and equilibration. Pass at 70% to earn a verifiable StemSkills certificate. Download it as a PDF and add it to your LinkedIn profile. It is free.

Molecular Dynamics (GROMACS) certification assessment

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