Paper Citing NAMD - Abstract
Coveney, P. V.; Sadiq, S. K.; Saksena, R. S.; Zasada, S. J.
Constructing chained molecular dynamics. Simulations of HIV-1 protease using the application hosting environment
Proceedings of the UK e-Science All Hands Meeting 2006, 428-431, 2006
Many crystal structures of HIV-1 protease exist, but the number of clinically interesting drug resistant mutational patterns is far larger than the available crystal structures. Mutational protocols convert one protease sequence with available crystal structure into another that diverges by a small number of mutations. It is important that such mutational algorithms are followed by suitable multi-step equilibration protocols, e.g. using chained molecular dynamics simulations, to ensure that the desired mutant structure is an accurate representation. Previously these have been difficult to perform on computational grids due to the need to keep track of large numbers of simulations. Here we present a simple way to construct a chained MD simulation using the Application Hosting Environment.
