protein stimulation

August 7, 2012

Images showing the conformational space explored by the protein in the 1ms conventional MD Anton simulation, and the 500ns aMD simulation. The red diamond marks the crystal structure where both simulations were started from; the triangles represent important structures found in the 1ms simulation. The lower image shows that with a single graphics card running 500ns of accelerated MD, the same structures can be sampled and the same relative conformational space can be explored. Principal Component Analysis (PCA) captures the slowest motions of the protein, which correspond to conformational changes on long timescales. Moving L to R along the x-axis captures the primary slow rocking motion of the protein; moving vertically on the y-axis captures the second slowest motion, or wagging movement. Courtesy of the Walker MD Lab, San Diego Supercomputer Center.