Practical notes derived from the theorem of Molecular Dynamics
- Force fields in YASARA
- AMBER: 5 essential parts, good for explicit solvents no in vacuo
- YAMBER-AMBER: AMBER adapted for yasara good for long protein simulations
- YASARA/YASARA2: Best for homology modelling. uses dihedral potentials
- YAMBER3:
- What were using with a 7.86 anstrom cutoff for vdW forces only
- long range electrostatic uses coulombs law via Wwalds algorithm
- made for long simulations.
- vdW interactions are a little stronger to eliminate holes in structure building
- Prepare structure for simulation
- Add hydrogens, solvate it, eliminate gps, eliminate steric clashes
- Check amide sidechain orientation (Asn/Gln) because hydrogen is ambiguous
- Check atom assignments of histidine assignments because Carbon vs Nitrogen is difficult
- Final minimization
- Dunk it in a box bound, usually water box
- Some programs have to specify which cysteines are bridged
- Initial state
- position r is from experimental (crystallographers or QM)
- velocities are random values in boltzman distribution modulated by temperature
- Simulation
- initial state r and v
- sum of forces are vector F on each atom via force field
- calculate accelerations from newtons 2nd law
- use a small time interval dt
- calculate dv = integral(a x dt)
- new velocity vector v’ = v + dv
- new positions r’ = r + v’ dt
- take new r’ and v’ and return to step 2
- Periodic boundary conditions
- every time an atom exits from boundary conditions of the cell, an identical one of same type enters from opposite side with same velocity
- Equilibration
- Have to wait for the system to equilibrate at the given temperature because initial V are random
- this means you can’t use the first part of the simulation
- for protein you dump the first nanosecond
- for peptide this doesn’t take as long, 100-300 picoseconds
- you know when Heavy Atom root mean standard deviation (HA_rmsd) plotted over time should equilibrate
- Energy should be pretty constant over time