As announced some time ago we have been working on a new core (Protomol core B4), and it has been looking good in QA so we have started to release Promol core WUs more broadly. We have a preliminary Protomol FAQ for those who are curious to get more information.
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.
The new projects are distributed by a new server (220.127.116.11) 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.