Paper Citing NAMD - Abstract
Phillips, S.C.; Swain, M.T.; Wiley, A.P.; Essex, J.W.; Edge, C.M.
Reversible digitally filtered molecular dynamics
JOURNAL OF PHYSICAL CHEMISTRY B, 107:2098-2110, MAR 6 2003
It has recently been shown that digital filtering methods may be used to selectively enhance or suppress the vibrational motion in a molecular dynamics computer simulation solely on the basis of frequency (J. Chem. Phys. 2000, 112, 2586-2597). The method of digitally filtered molecular dynamics (DFMD) does, however, suffer from a number of disadvantages, the most important of which is the rapid redistribution of energy from the selected frequency range in condensed phase simulations. Here, an extension of the DFMD method that solves this problem, reversible digitally filtered molecular dynamics (RDFMD), is presented. In RDFMD, the digital filter is applied successively to velocities that have been generated from previous applications of the filter, by the simple expedient of running simulations both forward and backward in time to fill the filter buffer after each filter application. In this way, kinetic energy is added slowly to the system, with the result that the conformational transitions observed are more controlled and realistic. The method is applied to a number of systems of increasing complexity including alanine dipeptide in gas and condensed phases. These studies demonstrate the advantage of adding energy gradually and also reveal a change in the characteristic frequency of critical vibrations as the transition state is approached. A protocol for applying RDFMD to protein systems has also been devised and tested on the YPGDV pentapeptide in water.
