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Free Molecular Dynamics (GROMACS) Certification Assessment

StemSkills Lab > Free Molecular Dynamics (GROMACS) Certification Assessment

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