Release of new Protomol (Core B4) WUs

[PcPerf bot]

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:

 

<ul class="bb_ul"><li class="bb_li">To validate NML by simulating the folding and dynamics of the Fip35 WW domain.

 

<li class="bb_li">To understand the role of mutations on folding.

 

<li class="bb_li">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 (129.74.85.48) which is located at the University of Notre Dame (Indiana) and have the following characteristics:

<ul class="bb_ul"><li class="bb_li">p10000 : 544

atoms, 84.48 points, preferred deadline 3.07 days, final deadline 23.04

days. This project uses conventional simulation methods.

<li class="bb_li">p10001 : 544 atoms, 50.56 points, preferred

deadline 1.84 days, final deadline 13.79 days. This project uses the

NML simulation method.

We will be posting more information as time goes on.   I'm very excited about the new capabilities here, since NML allows us to algorithmically get an amazing speed up, i.e. without any additional CPU power.    That algorithmic speed up multiplied by the vast power of FAH could mean very significant advances shortly, making 2010 an exciting year for FAH (in many ways)!

 

 

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