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More than Virtual Reality: Important New Physical Insights in Simulations of Biomolecules and Synthetic Polymers
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predict, and/or inspire real world biochemical or biophysical experiments. While the second and third criteria also apply to studies of synthetic polymers, there are two additional factors that play a crucial rule here. The first one is that for synthetic polymers it is even more important for the force fields to be vetted via comparison with experimental data. The vast majority of offthe-shelf force fields were developed for biomolecules or liquids composed of small molecules. A small quantitative error in the interaction between two monomers can have a qualitative effect on the properties of a polymer. This is because the structural and thermodynamic properties are very sensitive to these interactions. For example, a mixture of hydrogenated and deuterated polymers, e.g., polyethylene, can be immiscible even though at the monomer level dispersion interactions differ by less than 2%. The second factor is that equilibration is most important here. With synthetic polymers, one is usually interested in conformational properties and care has to be taken that the simulations have sampled the configurational space adequately. A simulation that is long enough for a folded protein or a small peptide could be woefully inadequate for a synthetic polymer. For example, the relaxation times of short 20-monomer poly(ethylene oxide) oligomers in an ionic liquid may reach tens of microseconds. We hope that the above paragraphs will help you as authors to decide beforehand whether your report on biomolecular or synthetic polymer simulations stands a chance to be published in the Journal of Physical Chemistry. Whenever the answer is yes, we look forward to exciting submissions!
e all love watching molecules move on the computer screen! The colors are bright, the contours are sharp, the motions are vivid, it is all so beautiful...and thus it must be true. But seriously, computer simulations are fantastic tools that can provide molecular insights with unprecedented spatial and temporal resolution. They are routinely employed in studies of biomolecules and synthetic polymers complementing, preceding, or sometimes even replacing experimental investigations. The number of submitted manuscripts dealing with these topics is increasing steadily. So, why do we often hesitate to publish such reports? For biomolecular simulations, the following three features make a study appealing for the readership of the Journal of Physical Chemistry: (i) a biochemically/biophysically relevant problem addressed, (ii) innovative molecular simulations competently executed, and (iii) direct relation to experiment established. Maybe the best way to demonstrate what we have in mind is to discuss negative examples lacking these features. Concerning the first point, choosing a biomolecule as the object of study does not automatically qualify the work as biologically relevant. Investigations of an ad hoc chosen single amino acid or a DNA base placed in a vacuum are unlikely to bring new biochemically or biophysically important insights. It is acceptable to simulate model systems; after all, none of us can simulate at a molecular level complex biological objects like a whole cell. However, the simplified simulated system must represent a faithful model of a biological functionality. Indeed, the keyword here is biological f unctionsimulating a biomolecule per se is not enough; one needs to address a biologically relevant question and provide a molecular level answer. Second, a report on a short molecular dynamics run employing the first available off-the-shelf force field is unlikely to meet the required standards for publication. Biomolecular simulations need to have both the systematic and statistical errors under control. The former requires careful testing of the employed interaction potentials against experiment and/or high quality electronic structure calculations on relevant model systems. The latter requirement of statistically converged results can rarely be satisfied by simply running the simulation a bit longer...and then again a bit longer. Instead, sophisticated methods enhancing phase space sampling often need to be employed in order to obtain reliable structural and, in particular, energetic data about the biomolecular system. Finally, a biomolecular simulation study that does not go into the effort of directly connecting to experiment is likely to be rejected and the authors will be advised to seek publication in a more specialized computational journal. Molecular simulations represent virtual reality. It is true that the boundaries between the real and virtual worlds are becoming more and more blurred nowadays and that simulations can sometimes be viewed as standalone computer experiments. Nevertheless, what we seek here are molecular simulation studies that interpret, © 2017 American Chemical Society
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Arun Yethiraj Pavel Jungwirth,* Senior Editors AUTHOR INFORMATION
ORCID
Arun Yethiraj: 0000-0002-8579-449X Pavel Jungwirth: 0000-0002-6892-3288 Notes
The authors declare no competing financial interest.
Published: July 6, 2017 6294
DOI: 10.1021/acs.jpcb.7b05957 J. Phys. Chem. B 2017, 121, 6294−6294
