Packmol

Packmol One of the biggest issues you face when you first start doing molecular dynamics (MD) simulations is how to create an initial geometry that won’t blow up in the first few time steps. Repulsive forces are very steep if the atoms are too close to each other, and if you are trying to simulate a condensed phase (liquid, solid, or interfacial) system, it can be hard to know how to make a sensible initial structure.

Packmol is a cool program that appears to solve this problem. It creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short range repulsive interactions do not disrupt the simulations. The great variety of types of spatial constraints that can be attributed to the molecules, or atoms within the molecules, makes it easy to create ordered systems, such as lamellar, spherical or tubular lipid layers. It works with PDB and XYZ files and appears to be available under the GPL. Very, very cool!

Reaching Agreement On The Public Domain For Science

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Photo outside the Panton Arms pub in Cambridge, UK, licensed to the public under Creative Commons Attribution-ShareAlike by jwyg (Jonathan Gray).

Today marked the public announcement of a set of principles on how to treat data, from a legal context, in the sciences. Called the Panton Principles, they were negotiated over the summer between myself, Rufus Pollock, Cameron Neylon, and Peter Murray-Rust. If you’re too busy to read them directly, here’s the gist: publicly funded science data should be in the public domain, full stop.

If you know me and my work, this is nothing new. We have been saying this since late 2007. I’ve already gotten a dozen emails asking me why this is newsworthy, when it’s actually a less normative version of the Science Commons protocol for open access to data (we used words like “must” and “must not” instead of the “should” and “should not” of the principles).

It’s newsworthy to me because it represents a ratification of the ideals embodied in the protocol by two key groups of stakeholders. First, real scientists – Cameron and Peter are two of the most important working scientists in the open science movement. Getting real scientists into the fold, endorsing the importance of the public domain, is essential. They’re also working in the UK, which has some copyright issues around data that can complicate things in a way we forget about here in the post-colonial Americas.

Second, it’s newsworthy because Rufus and I both signed it. Rufus helped to start the Open Knowledge Foundation, and he’s an important scholar of the public domain. We’re in many ways in the same fraternity – we care about “open” deeply, and we want the commons to scale and grow, because we believe in its role in innovation and creation…indeed, in its role in humanity.

But we’re on different sides of a passionate debate about data and licenses. I’m not going to recapitulate it here, you can find it in the googles if you want. Suffice to say we have argued about the role of the public domain as a first principle in general for data, as opposed to the specifics of data in public funded science. But for both of us to sign onto something like this means that even in the midst of heated argument we can find common ground – public money should mean public science, no licenses, no controls on innovation and reuse, globally.

It’s important for the science part. It’s also a good lesson, I hope, that even those of us who find themselves on opposite sides of arguments inside open are usually fighting for the same overall goals. I’ll keep arguing for my points, and Rufus will keep arguing for his, but that should never keep us from remembering the truly common goals we share inside the movement. I’m proud to be a part of it.

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Open Access Mandates and the “Fair Dealing” Button

Sale, A., Couture, M., Rodrigues, E., Carr, L. and Harnad, S. (2010) Open Access Mandates and the “Fair Dealing” Button. In: Dynamic Fair Dealing: Creating Canadian Culture Online (Rosemary J. Coombe & Darren Wershler, Eds.)

ABSTRACT: We describe the “Fair Dealing Button,” a feature designed for authors who have deposited their papers in an Open Access Institutional Repository but have deposited them as “Closed Access” (meaning only the metadata are visible and retrievable, not the full eprint) rather than Open Access. The Button allows individual users to request and authors to provide a single eprint via semi-automated email. The purpose of the Button is to tide over research usage needs during any publisher embargo on Open Access and, more importantly, to make it possible for institutions to adopt the “Immediate-Deposit/Optional-Access” Mandate, without exceptions or opt-outs, instead of a mandate that allows delayed deposit or deposit waivers, depending on publisher permissions or embargoes (or no mandate at all). This is only “Almost-Open Access,” but in facilitating exception-free immediate-deposit mandates it will accelerate the advent of universal Open Access.

The Immediate Practical Implication of the Houghton Report: Provide Green Open Access Now

Harnad, S. (2010) The Immediate Practical Implication of the Houghton Report: Provide Green Open Access Now. Prometheus 28 (1): 55-59

ABSTRACT: Among the many important implications of Houghton et al?s (2009) timely and illuminating JISC analysis of the costs and benefits of providing free online access (?Open Access,? OA) to peer-reviewed scholarly and scientific journal articles one stands out as particularly compelling: It would yield a forty-fold benefit/cost ratio if the world?s peer-reviewed research were all self-archived by its authors so as to make it OA. There are many assumptions and estimates underlying Houghton et al?s modelling and analyses, but they are for the most part very reasonable and even conservative. This makes their strongest practical implication particularly striking: The 40-fold benefit/cost ratio of providing Green OA is an order of magnitude greater than all the other potential combinations of alternatives to the status quo analyzed and compared by Houghton et al. This outcome is all the more significant in light of the fact that self-archiving already rests entirely in the hands of the research community (researchers, their institutions and their funders), whereas OA publishing depends on the publishing industry. Perhaps most remarkable is the fact that this outcome emerged from studies that approached the problem primarily from the standpoint of the economics of publication rather than the economics of research.

Houghton, J.W. & Oppenheim, C. (2009) The Economic Implications of Alternative Publishing Models. Prometheus 26(1): 41-54

Houghton, J.W., Rasmussen, B., Sheehan, P.J., Oppenheim, C., Morris, A., Creaser, C., Greenwood, H., Summers, M. and Gourlay, A. (2009). Economic Implications of Alternative Scholarly Publishing Models: Exploring the Costs and Benefits, London and Bristol: The Joint Information Systems Committee (JISC)