Threading energy

Click the little arrow beside the question mark of the Alignment window to view a plot of threading energies. 

As noted above, one of the goals of NAMD 2 is to take advantage of clusters of symmetric multiprocessor workstations and other non-uniform memory access platforms. This can be achieved in the current design by allowing multiple compute objects to run concurrently on different processors via kernel-level threads. Because compute objects interact in a controlled manner with patches, access controls need only be applied to a small number of structures such as force and energy accumulators. A shared memory environment will therefore contribute almost no parallel overhead and generate communication equal to that of a single-processor node. 

Bryant S H and C E Lawrence 1993. An Empirical Energy Function for Threading Protein Sequences Through the Folding Motif. Proteins Structure, Punction and Genetics 16 92-112. 

Jones D T and J M Thornton 1996. Potential Energy Functions for Threading. Current Opinion in Structural Biology 6 210-216. 

SH Bryant, CE Lawrence. An empirical energy function for threading protein sequence thi-ough the folding motif. Pi-otems Struct Eunct Genet 16 92-112, 1993. 

Jones, D.T., Thornton, J. Potential energy functions for threading. Curr. Opin. Struct. Biol. 6 210-216, 1996. 

As noted, biological systems are too complex for deriving an expression for free energies from first principles. Consequently, the common thread through... 

Threading of the protein through a membrane requires energy and organellar chaperones on the trans side of the membrane. 

The master thread performs all the intemode communication using MPI. Only the action of the kinetic energy operators, Tr and Tr implemented with the DFFD approach, require such communication. While the master thread is executing the communication part and storing its results in hpsbuff, other threads perform local work storing results in the main array hps local. The use of the two separate arrays is needed to avoid having to synchronize the threads. Moreover, if the communication part finishes before the local part, the master thread joins the other threads in the computation of the local part. 

The shared memory OpenMP library is used for parallelization within each node. The evaluation of the action of potential energy, rotational kinetic energy, and T2 kinetic energy are local to each node. These local calculations are performed with the help of a task farm. Each thread dynamically obtains a triple (/2, il, ir) of radial indices and performs evaluation of first the kinetic energy and then the potential energy contribution to hps local( , i2, il, ir) for all rotational indices. 

Figure 21. Boundaries of the energy-momentum map for the resonant 1 1 2 oscillator, with a central singular thread. Taken from Ref. [13] with permission of the American Institute of Physics, Copyright 2004.

The next three chapters deal with the most widely used classes of methods free energy perturbation (FEP) [3], methods based on probability distributions and histograms, and thermodynamic integration (TI) [1, 2], These chapters represent a mix of traditional material that has already been well covered, as well as the description of new techniques that have been developed only recendy. The common thread followed here is that different methods share the same underlying principles. Chapter 5 is dedicated to a relatively new class of methods, based on calculating free energies from nonequilibrium dynamics. In Chap. 6, we discuss an important topic that has not received, so far, sufficient attention - the analysis of errors in free energy calculations, especially those based on perturbative and nonequilibrium approaches. 

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