Dears, we are happy to announce that the results of various GPUGRID-enabled studies were recently published in high-impact journals.

The first one I'd like to mention is "A high-throughput steered molecular dynamics study on the free energy profile of ion permeation through gramicidin A". The paper is a numerical investigation on the convergence of a molecular dynamics (MD) technique called "steered MD" (SMD), which is used to obtain free energy profiles (i.e. probabilities of occurrence of certain biological events). The SMD technique is essentially based on statistics: one has to repeat the same experiment (computational or otherwise) over and over, many times, until a reliable result is obtained. How many times, and how reliable? Up to now, studies performed SMD on biologically-realistic systems were limited to just a few (~10) trajectories, and the corresponding error was therefore hard to assess. We used GPUGRID to perform increasing number of pulls, up to two thousands, to verify how much the precision of a free energy profile was gradually improved as a consequence. (The answer, if you were wondering, is that one needs quite a lot of simulations).

T. Giorgino and G. De Fabritiis, A high-throughput steered molecular dynamics study on the free energy profile of ion permeation through gramicidin A, in press J. Chem. Theory Comput. (2011).

Thanks to all of the crunchers of the GA* series of workunits!

Congratulations on publishing another pioneering piece of research. Well done Toni, Gianni, your lab colleagues and all the crunchers that chipped in.


Abstract

Steered molecular dynamics (SMD) simulations for the calculation of free energies are well suited for high-throughput molecular simulations on a distributed infrastructure due to the simplicity of the setup and parallel granularity of the runs. However, so far, the computational cost limited the estimation of the free energy typically over just a few pullings, thus impeding the evaluation of statistical uncertainties involved. In this work, we performed two thousand pulls for the permeation of a potassium ion in the gramicidin A pore by all-atom molecular dynamics in order to assess the bidirectional SMD protocol with a proper amount of sampling. The estimated free energy profile still shows a statistical error of several kcal/mol, while the work distributions are estimated to be non-Gaussian at pulling speeds of 10 Å/ns. We discuss the methodology and the confidence intervals in relation to increasing amounts of computed trajectories and how different permeation pathways for the potassium ion, knock-on and sideways, affect the sampling and the free energy estimation.

http://vimeo.com/3173968