We propose to continue the design, building and programming of Transputer- based parallel computers for molecular modelling, and to develop parallel programming techniques for molecular simulations and other simulations in Medical Science, e.g. for Magnetic Resonance Imaging. These technique allow the simulation of much larger systems than had been possible sofar, e.g. protein complexes with several 10 000 atoms, and dramatically improve the price/performance ratio of simulation calculations. The computer and its program will be based on the MIMD concept which allows that each processor in a parallel computer runs its own program, and which is most suitable for simulation of heterogeneous biopolymer systems. We intend to delegate only the force evaluation and integration of equations of motion to parallel computers, and to employ existing programs for visualization as well as for data preparation and analysis. For this purpose we will interface the parallel computer and its program to the software packages Quanta and CHARMM/XPLOR of Polygen Corp, and we will adapt the Iris molecular graphics workstations of Silicon Graphics as a host for the parallel computer. As a platform for program development we will port the LogixOS operating system and its Fortran complier of Topologix Inc. to the Iris workstation. We will add several capabilities to the parallel simulation program, including a new approximation for Coulomb interactions, hydrophilic and hydrophobic interactions, stochastic, and presentations of forces near polymer-water-membrane interfaces. A main goal is to make a single board as well as a multi-board parallel computer together with appropriate, modifiable software packages available to other molecular modeling researchers.
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