Criteria

Validation items

1. The quality of the theory or model used
   Explain clearly the assumptions used, how the results are obtained, and why the theory/model is appropriate.
2. The accuracy of the force field
   Specify functional forms and parameters or provide a complete reference. Are their any tests, current or prior, that justify use of the force field?
3. Sampling, statistics, convergence
   Specify all pertinent parameter values, explain how the sampling is done, provide an uncertainty analysis, and measures of convergence.
4. Is the software correct?
   Explain why the software used is appropriate for the problem.
5. Is the software used properly?
   Discuss/provide checks for physically consistent/sensible outputs.  Are the parameters sensible? Are there any unphysical correlations?
   

A checklist for authors of molecular dynamics and Monte Carlo simulations

MD specific:

• Integration algorithm
• time step
• coupling parameters for thermostats, barostats, etc.

MC specific:

• Types of moves employed
• acceptance ratios
• Are move steps and intervals fixed or adaptive?
  

Both:

• Ensemble used. Any special parameters?
• System size and composition
• Molecular structure including intramolecular interactions and constraints
• Force field including functional forms and all parameters or a
• complete reference that is readily available.
• Convergence criteria such as a time series analysis
• Sampling details
• Uncertainty analysis
  

Key Journals

We consider three levels of journals:
Level 1 are major journals that publish many articles involving molecular simulation.
Level 2 are important journals that occasionally publish such articles.
Level 3 are trade publications that cater to management.

Level 1

• Journal of Chemical Physics
• Journal of Physical Chemistry A
• Journal of Physical Chemistry B
• Molecular Physics
• Molecular Simulation
• Fluid Phase Equilibria
• International Journal of Thermophysics
• Journal of the American Chemical Society
• Langmuir
• Biophysical Journal
• Physical Chemistry Chemical Physics
• AIChE Journal
• Physical Review E
• Journal of Chemical Theory and Computation

Level 2

• Soft Matter
• Chemical Physics
• Chemical Physics Letters
• Proteins
• Biopolymers
• Biophysical Chemistry
• Polymer
• Journal of Molecular Liquids
• Biochemistry
• Physical Review Letters
• Journal of Colloid and Interface Science

Level 3