Simbios Talk by JesÃºs A. Izaguirre, University of Notre Dame, May 27, 2009
In this method the higher frequency modes are minimized while respecting the subspace of low frequency dynamical modes, which are accurately propagated. The method periodically recomputes the normal modes using a coarse-grained normal mode analysis (CNMA) that captures the essential features of the low frequency modes. CNMA scales as O(N log N) time and O(N) memory, thus retaining the potential efficiency increase of the underlying NML method. NML is capable of accommodating large conformational change of proteins, as shown in simulation of WW domain folding. For this example NML is capable of using time steps of 50 to 100 fs, with real speedups of 17 to 33 over plain Langevin dynamics. Speedups are larger for larger proteins. |

Feedback ---- Collaborations ---- Career ---- Administration ---- Contact |