Metadynamics Free Energy Surface of a Capped Dipeptide¶
- Task ID:
chemistry.metadynamics_for_dipeptide_in_vacuum - Domain:
chemistry - Subdomain:
molecular_simulation - Status:
test - Tags:
metadynamics,well_tempered,free_energy_surface,val_dipeptide,dihedral_angles,enhanced_sampling,molecular_dynamics,openmm,ramachandran
Public Summary¶
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Example B1 Prompt Excerpt¶
# Metadynamics Free Energy Surface of {{ dipeptide_name_title }} Dipeptide
You are given the initial atomic coordinates of a capped dipeptide in `data/dipeptide.pdb`. Your task is to compute the 2D conformational free energy surface (FES) as a function of the backbone dihedral angles phi and psi using well-tempered metadynamics in vacuum.
## System setup
- **Force field**: AMBER ff14SB (`amber14-all.xml` in OpenMM)
- **Environment**: Vacuum (no solvent, no periodic boundary conditions, use `NoCutoff`)
- **Temperature**: {{ temperature }} K
## Collective variables
Define two collective variables (CVs):
Notes¶
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- Higher-level prompt details and internal benchmark specifics may remain intentionally undisclosed.