Protomol core unveiled with -advmethods

By , the in Folding@Home Project - 6 Comments
The Protomol core for uniprocessor clients has just entered the public testing phase for –advmethods flag users. It comes along with two new projects: 10000 and 10001.

This new core implements the NML (Normal Mode Langevin) method which accelerates the long-time dynamics of the proteins by a factor that can reach speeds up to a hundred times faster than those of molecular dynamics. This method searches for low frequency directives by using normal mode analysis and projects the motion of the molecule along them while resolving the nearly instantaneous motion. If you want to learn more about this method, you should read this pre-publication: Multiscale Dynamics of Macromolecules Using Normal Mode Langevin.

Based on Protomol 3.1, this core and its associated projects have the following goals:

  • To validate NML by simulating the folding and dynamics of the Fip35 WW domain.
  • To understand the role of mutations on folding.
  • To understand the activation of src Kinase, an enzyme that is involved in the onset of some kinds of cancer.

On the technical side, this core is able to take advantage of most modern CPU optimizations (SSE2, SSE3, SSSE3, SSE4.1 and SSE4.2), however, a few compatibility issues are still present on AMD processors, resulting in the core only using SSE2 on these chips. This should change in the not-too-distant future when the issues have been worked out. If you have a processor that doesn’t have the above mentioned optimizations (Pentium 3, Athlon XP, etc.), please report the behavior and the performance of this core on your machine.

For more information about the Protomol core, you should visit the Protomol official site.

The new projects are distributed by a new server ( which is located at the University of Notre Dame (Indiana) and have the following characteristics:

  • p10000 : 544 atoms, 84.48 points, preferred deadline 3.07 days, final deadline 23.04 days. This project uses conventional simulation methods.
  • p10001 : 544 atoms, 50.56 points, preferred deadline 1.84 days, final deadline 13.79 days. This project uses the NML simulation method.

Updated on 22 Dec at 22H15 UTC :
The behaviour of Project 10001 has proven to be different from that which we usually see; sometimes, the simulation enters into a state where no further computation is possible, but which is not technically a folding error. This situation usually triggers, with other cores, an Early_Unit_End or an Unstable_Machine error. With the Protomol core, these states are expected and don't trigger an error. You'll see them with a WU reported as completed (Finished unit, core status = 64) before it reaches 100%. Don't worry if this phenomenon occurs on your machine; it is perfectly normal and expected.

Happy folding!