<p>This report describes the work of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics, Third Round. The committee evaluated submissions received in response to a request for proposals for biomolecular simulation time on Anton, a supercomputer specially designed and built by D.E. Shaw Research (DESRES) that allows for dramatically increased molecular dynamics simulations compared to other currently available resources. These special capabilities allow multi-microsecond to millisecond simulation timescales, which previously had been unobtainable. Over the past two years (October 1, 2010 ?" September 30, 2012), DESRES has made available to the noncommercial research community node-hours on an Anton system housed at the Pittsburgh Supercomputing Center, based on the advice of previous National Research Council committees convened in the fall of 2010 and 2011. The success of the program has led DESRES to make the Anton machine available for an additional 3,700,000 node-hours over the 9 months following October 2012, and DESRES asked the National Research Council to once again facilitate the allocation of time to the noncommercial research community.</p> <p><i>Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics, Third Round</i> is the report of the committee's evaluation of proposals for time allocations in order to continue to facilitate breakthrough research in the study of biomolecular systems. The committee sought to continue to support research that addresses important and high impact questions demonstrating a clear need for Anton's special capabilities. The committee evaluated proposals based on scientific merit, justification for requested time allocation, and investigator qualifications and past accomplishments. This report identifies the proposals that best met the selection criteria.</p>