Protein simulation can be done three times as fast

Protein movement can be simulated three times as fast than had been thought possible up to now. Researchers from Groningen achieved the gain in speed by leaving out the calculations concerning hydrogen atoms. Meanwhile research groups around the world are adapting their simulation programs.

Up until now researchers calculated all of the positions of atoms in a protein molecule after two femtoseconds. A femtosecond is one millionth of a billionth of a second. The research from Groningen reveals that steps of 7 femtoseconds are also good enough. With this the simulation is three times as fast. A number of research groups are already using the results from the Groningen study.

Steps of 7 femtseconds ignore the forces which occur between hydrogen atoms. The researchers have demonstrated that these forces are not relevant for the simulation. Indeed, taking into account how the forces were always described up until now, they are best left out of the calculations.

PhD student Anton Feenstra: “The forces around hydrogen atoms are so small that they cannot really be calculated according to the standard billiard ball description. However, up until now we did do this. If you really want to include hydrogen, although I have shown that does not really need to be done, you should describe it using quantum mechanics.”

The researchers expect that the intervals will not become much greater than 7 femtoseconds. Even greater intervals result in unrealistic situations. For example, particles come so close together that it is no longer natural and during the next interval they are further apart than is actually possible.

Biologically interesting processes such as the folding of proteins, occur in a matter of milliseconds. For this the fastest Pentium has to calculate day and night for 200 years. Supercomputers can perform these calculations about 100 times faster. Researchers expect that supercomputers will be so fast in ten years time that they will be able to perform these calculations in one week.