Overview
The current features of PumMa include:
- Lennard-Jones Van der Waals interactions
- Tabulated potentials (can also be read from file)
- Van der Waals 1-3 or 1-4 exclusion (through scaling)
- Coulombic electrostatic interactions (based on a cutoff)
- Bonded interactions (harmonic)
- Angle interactions (both cosine harmonic and harmonic)
- Urey-Bradley angle interactions
- Dihedral interactions (both cosine series and harmonic)
- Improper torsion interactions (harmonic)
- Energy minimization subroutine
- Verlet Leapfrog integration scheme
- Velocity Verlet integration scheme
- Bruenger-Brooks-Karplus integration scheme
- Berendsen temperature and pressure coupling
- Langevin dynamics
- Simulated annealing
- Separated heat baths (with Berendsen temperature coupling)
- Constant velocity steering of particles
- Periodic boundary conditions (only orthorombic systems)
- Fixed atoms
- External SI-units and internal reduced units
- PumMa forcefield
- CHARMM forcefield
- GROMOS96 forcefield
- Per interaction pair Lennard-Jones energy analysis
- Macroscopic quantity analysis along one of the box axis