Chemistry: Power play

Abstract

on computers running hundreds of parallel microprocessors to simulate how individual atoms behave in proteins and other large molecules. Schulten's group itself was working on a million-atom model of the satellite tobacco mosaic virus, which the researchers called "the first all-atom simulation of an entire life form" 1 .But the German-born physicist got his wakeup call in 2006, when he saw a table of computing benchmarks in a report from that year's supercomputing conference in Tampa, Florida. A new program called Desmond, he saw, could calculate each step of a standard moleculardynamics simulation -the 23,558 atoms in a system involving the protein dihydrofolate reductase -in a little over a thousandth of a second. NAMD was ten times slower. "Suddenly, "Schulten says, "we were not the best anymore. "The title had passed to the sender of the chocolates -David Shaw, a hedge-fund magnate and computer expert who taught himself physical chemistry. Over the previous few years, he had recruited more than 50 scientists and engineers, including three former students from Schulten's group, and put them to work in his midtown Manhattan high-rise.In the paper from the supercomputing conference, Shaw's team wrote that Desmond "is faster than NAMD at all levels of parallelism examined" 2 . And the group noted that on one simulation Desmond ran faster on 1,024 processors than NAMD ran on the 16,384 processors of IBM's Blue Gene/L -the world's fastest supercomputer.A German physicist and a hedge-fund magnate are competing to push protein simulations into the realm of the millisecond. Brendan Borrell finds out what is at stake.

Dissipative Particle Dynamics Simulations for Phospholipid Membranes Based on a Four-To-One Coarse-Grained Mapping Scheme

“…Computer simulations can provide detailed information to elucidate how small changes in local conformation propagate to affect the properties of macromolecular complexes. In principle, the widely used all-atom molecular dynamics (AAMD) simulation can provide insight into the links between structures and physical properties [ 1 ]. However, the assembly of complex biomolecular systems usually spans length and time scales far beyond the molecular scales [ 2 , 3 ].…”

Technical advances in molecular simulation since the 1980s

“…In the molecular domain most work appears to have been done on chips for accelerating MD simulations with molecular mechanical (MM) force fields. Examples include the FASTRUN accelerator of Fine et al [6], the Gemmstar project of Brooks et al [7] that was being undertaken by the author's host group when he was at the NIH, and the MDGRAPE series of processors that are currently in their fourth incarnation [8,9]. The problem with these efforts is that the production of specialized chips is extremely demanding and so can be very slow in a niche market such as that for MD simulations unless substantial resources are provided.…”

BiomolekulareSimulationen

“…Wohl nur wenige Arbeitsgruppen auf der Welt haben Zugang zu derartigen Rechnerresourcen. Für Ende dieses Jahres hat dasselbe Unternehmen jedoch einen neuartigen Rechner angekündigt, dessen Architektur speziell auf die Anfordernisse von MD‐Simulation zugeschnitten ist und Simulationen auf der Zeitskala von Millisekunden möglich machen soll − ein Quantensprung verglichen mit dem heutigen Stand 19.…”