Visual and Steered MD

The genomic phase of biology is giving way to a "structural phase", fueled by the 18,000 and rapidly multiplying structures already available in the protein data bank. The issue most often mentioned today is finding functions of proteins; however, the physical mechanisms underlying these functions remain central to basic life science and applied medicine. While molecular modeling is an ideal tool in this respect, since it complements observation and provides biopolymer properties in atomic-level detail, it still has not overcome the limitations to short time scales and the frequently voiced concern regarding ease-of-use.

Our development efforts ( VMD, NAMD, and BioCoRE) embrace the needs and requirements of the large and diverse community of life scientists who would be able participate in solving biopolymer mechanisms once molecular modeling becomes a commonly used tool. The time scale gap would be overcome by permitting the user to manipulate biopolymers in Steered Molecular Dynamics simulations by applying external forces. For this purpose one would select external forces that accelerate thermally activated processes in the native system. Ease of use would be achieved through combining molecular graphics and molecular dynamics, and thereby providing a user interface that would make molecular dynamics as friendly as molecular graphics is today.

To realize steered molecular dynamics several objectives have to be met:

  • A natural user interface that automates the initiation of molecular dynamics simulations needs to be developed, requiring advances in generation of proper pdb files, topology files, and force field parametrization.
  • Natural paradigms for user commands and visual feedback need to be developed.
  • Molecular dynamics simulations need to become fast enough that biopolymer systems of non-trivial size can be simulated with quick responses to user manipulation, e.g., 1 ps simulation time should be completed in 1 s wall clock time.
  • A haptic interface that facilitates manipulations through six degrees of freedom input and force feedback must be integrated into the user interface.
  • The results of steered molecular dynamics simulations need to be analyzed in terms of potentials of mean force and other properties that are relevant for slow processes, e.g., frictional work needs to be discounted from the simulation data (see here).

In pursuing these objectives Visual and Interactive Molecular Dynamics presents a great opportunity to advance life science by enabling the study of already available biopolymer structure information in order to explain life's processes. Reaching the full potential of Visual and Interactive Molecular Dynamics will require a decade of development on multiple fronts: graphics, parallel computing, human-computer interface design, non-equilibrium statistical mechanics, modular software design, and likely others, such as speech and gesture input. Our web site showcases the progress that has been made already and highlights key directions for further work.