Free Molecular Dynamics (GROMACS) Certification Assessment | StemSkills Lab
Skip to content
See live workshops

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
Sign in to see your result
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.
time left:
:
:

Molecular Dynamics (GROMACS) Certification Assessment

Submit quiz
Once you submit, you will no longer be able to change your answers. Are you sure you want to submit the quiz?
Cancel Submit

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

See the live cohort

See live workshops