Before revision:  However, the complexity of the high-dimensional space explored during dissociation on timescales that often exceed those accessible to conventional molecular dynamics (MD) simulations make this task highly challenging. Introduction of a scaling potential or additional force can accelerate the dissociation process, but may affect the reliability of simulated egress paths and thus observed mechanisms and computed residence times. We address this problem by exploring the dissociation of benzene and indole from T4 lysozyme mutants. We employ the tau-Random Acceleration Molecular Dynamics (tauRAMD) method , in which a small randomly oriented force is applied to the ligand to facilitate its unbinding during MD simulations.
After revision:  However, the complexity of the high-dimensional space explored during dissociation on timescales that often exceed those accessible to conventional molecular dynamics (MD) simulation. Here, we apply the tau-Random Acceleration Molecular Dynamics (tauRAMD) method , in which a small randomly oriented force is applied to the ligand to facilitate its unbinding during MD simulations.