| Genome Informatics 14: 625--626 (2003) 625 Parallelized Simulation of Molecular Dynamics with a (2008) | |||||||||||||||
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| Introduction Molecular dynamics (MD) simulation is a very useful technique for studying the structure and dynamics of biologically important molecules such as proteins and DNA/RNA. In MD simulations, each atom is treated as a classical particle. By MD simulation, we can treat the motion of molecules very precisely. However, we need high performance computational resources for the MD simulation of complex biomolecules. To overcome this di#culty, we have developed the special-purpose computer, MDGRAPE-2 [1] with high speed and accuracy. The most time consumed in the MD simulation is the calculation of non-bonded forces, i.e. Coulomb and van der Waals forces. The special-purpose computer MDGRAPE-2 accelerates the calculation of non-bonded forces. The calculation except of non-bonded forces is done by the host computer which is general-purpose computer. We have ported one of the most famous MD program packages for biomolecules, AMBER 6.0 [2] for using it on the MDGRAPE-2 board. In the pre | |||||||||||||||
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