Within molecular dynamics simulations of protein᎐solvent systems the exact evaluation of long-ran... more Within molecular dynamics simulations of protein᎐solvent systems the exact evaluation of long-range Coulomb interactions is computationally demanding and becomes prohibitive for large systems. Conventional truncation methods circumvent that computational problem, but are hampered by serious artifacts concerning structure and dynamics of the simulated systems. To avoid these artifacts we have developed an efficient and yet sufficiently accurate approximation scheme which combines the structure-Ž .w adapted multipole method SAMM C. Niedermeier and P. Tavan, J. Chem.
For the purpose of molecular dynamics simulations of large biopolymers we have built a parallel c... more For the purpose of molecular dynamics simulations of large biopolymers we have built a parallel computer with a systolic loop architecture, based on Transputers as computational units, and have programmed it in occam II. The computational nodes of the computer are linked together in a systolic ring. The program based on this topology for large biopolymers increases its computational throughput
EGO is a parallel molecular dynamics program running on Transputers. We conducted a performance a... more EGO is a parallel molecular dynamics program running on Transputers. We conducted a performance analysis of the EGO program in order to determine whether it was effectively using the computational resources of Transputers. Our first concern was whether communication was overlapped with computation, so that the overheads due to communication not overlapped with computation were less. With the assistance of performance tools such as UPSHOT, and with instrumentation of the EGO program itself, we were able to determine that only 8% of the execution time of the EGO program was spent in non-overlapping communication. Our next concern was that the MFLOPS rating of the EGO program was 0.25 MFLOPS, while the Transputers have a sustained rating of 1.5 MFLOPS. We measured MFLOPS ratings of small blocks of OCCAM code and determined that they matched the performance of the EGO code.
Membrane proteins and membrane related processes have been the subject of experimentalz-5 and the... more Membrane proteins and membrane related processes have been the subject of experimentalz-5 and theoretica1ll research during the past 40 years. The interest of the theoretical community in investigating biological membranes has been relatively low. One reason ...
. Molecular dynamics (MD) simulations of proteins provide descriptionsof atomic motions, which al... more . Molecular dynamics (MD) simulations of proteins provide descriptionsof atomic motions, which allow to relate observable properties of proteins to microscopicprocesses. Unfortunately, such MD simulations require an enormous amountof computer time and, therefore, are limited to time scales of nanoseconds. Wedescribe first a fast multiple time step structure adapted multipole method (FAMUSAMM)to speed up the evaluation of the computationally most
Membrane proteins and membrane related processes have been the subject of experimentalz-5 and the... more Membrane proteins and membrane related processes have been the subject of experimentalz-5 and theoretica1ll research during the past 40 years. The interest of the theoretical community in investigating biological membranes has been relatively low. One reason ...
Within molecular dynamics simulations of protein᎐solvent systems the exact evaluation of long-ran... more Within molecular dynamics simulations of protein᎐solvent systems the exact evaluation of long-range Coulomb interactions is computationally demanding and becomes prohibitive for large systems. Conventional truncation methods circumvent that computational problem, but are hampered by serious artifacts concerning structure and dynamics of the simulated systems. To avoid these artifacts we have developed an efficient and yet sufficiently accurate approximation scheme which combines the structure-Ž .w adapted multipole method SAMM C. Niedermeier and P. Tavan, J. Chem.
For the purpose of molecular dynamics simulations of large biopolymers we have built a parallel c... more For the purpose of molecular dynamics simulations of large biopolymers we have built a parallel computer with a systolic loop architecture, based on Transputers as computational units, and have programmed it in occam II. The computational nodes of the computer are linked together in a systolic ring. The program based on this topology for large biopolymers increases its computational throughput
EGO is a parallel molecular dynamics program running on Transputers. We conducted a performance a... more EGO is a parallel molecular dynamics program running on Transputers. We conducted a performance analysis of the EGO program in order to determine whether it was effectively using the computational resources of Transputers. Our first concern was whether communication was overlapped with computation, so that the overheads due to communication not overlapped with computation were less. With the assistance of performance tools such as UPSHOT, and with instrumentation of the EGO program itself, we were able to determine that only 8% of the execution time of the EGO program was spent in non-overlapping communication. Our next concern was that the MFLOPS rating of the EGO program was 0.25 MFLOPS, while the Transputers have a sustained rating of 1.5 MFLOPS. We measured MFLOPS ratings of small blocks of OCCAM code and determined that they matched the performance of the EGO code.
Membrane proteins and membrane related processes have been the subject of experimentalz-5 and the... more Membrane proteins and membrane related processes have been the subject of experimentalz-5 and theoretica1ll research during the past 40 years. The interest of the theoretical community in investigating biological membranes has been relatively low. One reason ...
. Molecular dynamics (MD) simulations of proteins provide descriptionsof atomic motions, which al... more . Molecular dynamics (MD) simulations of proteins provide descriptionsof atomic motions, which allow to relate observable properties of proteins to microscopicprocesses. Unfortunately, such MD simulations require an enormous amountof computer time and, therefore, are limited to time scales of nanoseconds. Wedescribe first a fast multiple time step structure adapted multipole method (FAMUSAMM)to speed up the evaluation of the computationally most
Membrane proteins and membrane related processes have been the subject of experimentalz-5 and the... more Membrane proteins and membrane related processes have been the subject of experimentalz-5 and theoretica1ll research during the past 40 years. The interest of the theoretical community in investigating biological membranes has been relatively low. One reason ...
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Papers by Helmut Heller