Reports on Normal Mode Integrators in Protomol.
Results from the implementation of Normal Mode Integrator in Protomol.
- Single water molecule simulations.
Comparison of eigenvalue and 'real force' Normal Modes for single water molecule.
- Alanine Dipeptide (Blocked 22-atom) simulations.
Expected maximum timestep for Alanine Dipeptide, compared to removed modes. Assumes 2.5fs timestep for normal MD.
- Alanine Dipeptide (Blocked 22-atom). Constrained modes with minimized mode forces, and ACTUAL coarsened simulation.
Highest frequency mode trajectory, using integrated and minimized force methods.
- Calmodulin. 4983 constrained modes with minimized mode forces, real forces at 3fs step.
Expected maximum speedup for Calmodulin.
- Calmodulin. 6000 constrained modes with minimized mode forces, real forces at 30fs step.
Calmodulin DCD, 120ps length, 30fs stepsize.
Calmodulin PSF file.
- Alanine Dipeptide (Blocked 22-atom). Normal Mode analytic visualization using 'NormModeVisual' propagator.
- Normal Mode analytic visualization without mass re-weighting.
Report including effect of conformation change on the Rayleigh Quotient.