[discuss ifpsc] Criteria for publication of molecular simulation papers
- From: IFPSC <admin@xxxxxxxxxxxxxxxxxxx>
- To: discuss-ifpsc@xxxxxxxxxxxxx
- Date: Fri, 2 Nov 2007 18:04:41 -0400
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.
Feel free to comment by replying to this email, by commenting on the
ifpsc webpage (http://fluidproperties.org/publication-criteria), or by
sending email directly to admin@xxxxxxxxxxxxxxxxxxxx
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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).
========================================================
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