Chignolin¶

Tested against md-tools 0.6.1. A ten-residue designed peptide that folds into a β-hairpin — the smallest system in this set with a real folding equilibrium.

Chignolin, 1UAO

Chignolin (PDB 1UAO, first NMR model), coloured from N to C terminus. The hairpin is the fold; the two termini sit side by side when it is formed.

Why this system¶

Folding and unfolding are slow compared with a torsion rotation but fast compared with a protein, so chignolin is where an enhanced-sampling method can be shown to reach a state that plain MD reaches only occasionally — and where the two can still be compared in a day.

1. The structure¶

mkdir -p CHI/build && cd CHI/build
curl -O https://files.rcsb.org/download/1UAO.pdb
awk '/^MODEL/{m++} m==1{print} /^ENDMDL/{if(m==1) exit}' 1UAO.pdb \
    | grep -E '^(ATOM|TER)' > chignolin.pdb
echo END >> chignolin.pdb

1UAO holds 18 NMR models; the build needs one. That leaves 138 atoms.

2. Build the system¶

build-top.config:

solute:
  kind: peptide
solvent:
  model: TIP3P
  padding_nm: 1.5
hydrogen_mass_repartitioning:
  enabled: true

md-openmm build-top -i chignolin.pdb -os built.xml -op built.pdb \
    -log built.log --config build-top.config

Writes the System, the structure that matches it and the build record. From built.log:

  atoms                       2553
  solute atoms                138
  waters                      803
  ions                        {'NA': 4, 'CL': 2}
  HMR                         applied, target 3.024 amu, recommend 4.0 fs

Four Na⁺ against two Cl⁻ because chignolin carries −2. What every key means: build-top.

Where to go next¶

method	what it is for
cMD	the unbiased reference, 1 ns at 4 fs with HMR	published
REST2	solute tempering over the whole peptide	published
AIS	annealed importance sampling	not written for this system
Umbrella sampling	a potential of mean force along an end-to-end distance	page planned, 0.6.5
Alchemical — ligand to ligand	free energies by transformation	planned, 0.6.5

Umbrella sampling arrives in 0.6.3 and the alchemical pages in 0.7.0. They are listed here so the shape of the set is visible; neither is written yet, and neither is linked to a page that does not exist.