Amber: LEAP to prepare force field and initial coordinate input files

Amber: automatically submit consecutive jobs

Take the example of triad MD simulation on the PI state. The strategy is suitable for equilibration or production runs. All the runs are along the same singl...

Amber: restart job with random initial velocities

Take the example of triad MD simulation on the GR state (similarly for CT1 and CT2 states). The strategy is suitable for perturbing the system by randomizing...

Github tutorials

Most useful git commands

How to extract energies from Amber output

Extract energies from the original Amber output file