CHARMM PORT -- HETEROGENEOUS IMPLEMENTATION

Charles Brooks and William Young

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Scientific Significance:

CHARMM is a widely used program to model and simulate molecular systems using an empirical potential energy function. In the 10 years since CHARMM was developed by Bernard Brooks and co-workers, a great deal of work has gone into developing optimized versions for a large number of computer systems including vector and parallel machines. The principal focus of most CHARMM-based research done by PSC users is simulating poly-peptides and proteins in an aqueous environment.

In particular, Alpha helices are one of the principle structural components of proteins. Using molecular dynamics simulations with umbrella sampling Brooks and Young have done free energy simulations of C-terminal and N-terminal helix propagation in small helices of AMN-(ALA)n-CBX, with n=(4,5,10,15), in water. In an upcoming MSI meeting they will present the results for propagating the helix by adding an additional hydrogen bond at the N-terminal and C-terminal ends of an existing alpha helix. Using these free energy surfaces, computed as a function of the terminal Y (phi) dihedral angle, they explored cooperativity and end effects in helix propagation. Analysis of the energetic components of the helices, both formed and partially formed, is used to develop a molecular rationalization of the observed trends in helix stability.

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Numerical Approach and Performance:

As a starting point we developed a specialized version of CHARMM for this problem and are currently running production calculations while we explore algorithms and methods for developing a full-featured version of CHARMM. This initial port extends ideas in heterogeneous computing previously explored at the PSC using a Cray Y-MP and a Thinking Machines Corporation CM-2 and CM-5. This heterogeneous computing approach couples the T3D and C90 over the high-speed channel using either DHSC routines or network PVM producing a highly-optimized code to simulate molecular solvents.

Heterogeneous CHARMM (2 Cases):

Apomyoglobin: 16K Atoms, 1 CPU + 32 T3D Processors = 2.3 C90 CPU's
Alanene Helix: 3K Atoms, 1 CPU + 32 T3D Processors = 3.0 C90 CPU's

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