These days it seems that molecular simulation papers are appearing in almost every scientific journal, and the documentation of these simulation methods in not always of consistently high quality. Therefore, the IFPSC wants to create a checklist of sorts for authors to use when writing papers and for reviewers to use when evaluating papers to help improve the overall quality of the scientific literature in this field. At the IFPSC workshop at 3M during the fall of 2006, Wilfred van Gunsteren and Ray Mountain developed a first draft of such criteria given below.

We invite you to review these criteria and make comments to improve them. What needs to be added? What is essential? What is only "nice-to-have?" etc.

Validation items

1. The quality of the 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 potential/force field. Specify functional forms and parameters or provide a complete reference. Are there any tests, current or prior, that justify use of the potential?
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?
   

Checklist
for authors of molecular dynamics and Monte Carlo simulations of items to be included in the validation discussion.

MD specific:

• Integration algorithm and time step used.
• Coupling parameters for thermostats barostats, etc.
  

MC specific:

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

Both:

• Version number if publicly-available code used
• 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 and widely available.
• Convergence criteria such as time series analysis or ergodic convergence metric
• Sampling details including number of samples and any limitations
• Uncertainty analysis
• Boundary conditions. Cell shape, rigid? flexible?
  

Examples of validation criteria in the literature:

W. F. van Gunsteren and A. E. Mark, "Validation of molecular dynamics simulations", J. Chem. Phys. 108, 6109 (1998).

S. E. Murdock, et al, "Quality assurance for biomolecular simulations", J. Chem. Theory Comput. 2, 1477 (2006).

Additional suggestions:

• J. Moore: Create a standard form/checklist to be populated with the info listed above and included in the supplementary info for simulation papers.  That way a reader would know where to go to quickly get this key information without annoyance of tracking down these details in the body of the paper which can sometimes be a "finding a needle in a haystack" type of activity.