Free Molecular Dynamics (GROMACS) Certification Assessment - StemSkills Lab
Have a question?
Send enquiry
Message sent Close

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