MOLDY is a MOLecular DYnamics based project focusing on the development and implementation of new algorithms with the aim of extending current molecular dynamics timescales. The project is funded throught the EU Marie Curie Host Fellowships for the Transfer of Knowledge (ToK) and started in August 2006.

Project description

The field of biomolecular and nanoscale modelling is currently in a critical phase of development which is driven, on the one hand, by advances in experimental methodologies, and on the other, by the availability of multi-teraflop scale computing. Experimental research is now providing unprecedented quantitative data on molecular processes at resolutions almost on an individual molecule scale. Computational power is now such that it is becoming possible to model interactions over the macroscopic timescales in which biomolecular processes occur. The challenge at this time is to combine experimental and computational approaches to fully elucidate the processes which drive molecular interactions.

The project consists of two core components:

• Research Component: The main goal of this component is the development and incorporation of new algorithms into established open source molecular dynamics (MD) codes. These algorithms will be evaluated using both biomolecular and solid-state models. In addition, there are three individual research projects headed by the three members of the MOLDY team. They are as follows:
  • Algorithm Development (Dr. Nava Whiteford)
  • Biomolecular Research (Dr. Justine Taylor)
  • Biomolecular Research (Dr. Matthew Ellis)
• ToK Component: In addition to the aforementioned research component this project also contains a "Transfer of Knowledge" or ToK component. The goal of this component is the dissemination of knowledge both to and from the aforementioned individual researchers. This includes transfer both within the MOLDY project as well to the greater scientific community (both within and outside of Trinity College). This transfer of knowledge may take the form of informal scientific discussions or of formal reports, lectures and courses. This component will result in the following deliverables:

• Benchmark Study
• Distribution of resulting tools to the wider scientific community. (See below)

Resulting Tools:

• Phospholipid Parameters: Topology files are based on the CHARMM27r force field (version c32b1) available here. Coordinate files are taken from the end of a 40 ns simulation, using a slightly modified charge set, resulting in a more accurate area per lipid. Each contains 200 lipids solvated in a TIP3P water box with 0.2M NaCl. Details will be published shortly.
  • DPPC: Topology, Coordinates(pdb)
  • POPC: Topology, Coordinates(pdb)
  • POPE: Topology
  • PDPC: Topology, Coordinates(pdb) (NAMD)
  • PDPC: PDPC.crd, frcmod.PDPC, prmtop (for AMBER)
• Membrane Analysis Tools: Tcl scripts can be used in the VMD TK Console by first sourcing them (i.e. source /filelocation/center.tcl) and then calling them with the requisite parameters.
  • Center bilayer (VMD Tcl script)
  • Membrane Width (VMD Tcl Script)
  • C++ tools: Readme File, tarred files