INSIGHT INTO BIOMOLECULAR STRUCTURE, DYNAMICS, INTERACTIONS AND ENERGETIC FROM

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. We propose to continue our studies of biomolecular structure, dynamics and interaction focusing on exposing and overcoming limitations in the empirical force fields and simulation methods. Our application areas center on nucleic acids and proteins, in their native environment, including interaction with other ligands, solvent, ions, and drugs. Our primary application code is AMBER and its specially optimized parallel version, PMEMD. Some studies involve NAMD or CHARMM as well.