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. Keywords: AMBER, molecular dynamics, protein, DNA Abstract: AMBER is a widely used computer program for molecular dynamics (MD) and free energy calculations for biomolecular systems. The major limitation in using such calculations to gain insights into biological systems is the restricted sampling of conformational space which can be done. The PSC has worked over the years with various AMBER authors to improve the efficiency of the code, particularly for implementation on parallel computers such as the CRAY T3D and CRAY T3E. The improvements are being incorporated into the official distributions of the software. In the next period, we plan to further improve the efficiency of the AMBER MD code, both building on the code developed by Duan, where we have begun to incorporate multiple timesteps (MTS) and long range electrostatics as well as including the exciting methods developed by Schlick et al, which should allow us to explore the use of longer timesteps in dynamic simulations governed by a stochastic framework. Tests of the LN method for NMR refinement will involve dynamic simulated annealing calculations for the TFIIIA-DNA 'zinc-finger' protein-DNA complex. Again, results will be compared to non-MTS runs to measure the ability of these models to sample configurational space (and to find optimum solutions to the NMR constraint problem), and to quantify the extent of improvement in computational efficiency that the MTS methods provide.
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