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cMD: Chinolin (quinoline) in explicit water

Archived: written for md-tools 0.5.3

This page was run against 0.5.3 and is kept as a record of that release. 0.5.4 changed the workflow it describes: REST2 states are built once, as files, by md-openmm build-top --rest2-scaler; a stage or a ladder no longer scales anything at run time, so a hot stage takes its saved state as -s and a ladder reads -s only from its group file; and more torsions stay unscaled (aromatic rings, double bonds and impropers, not only the amide omega). Commands here may be refused by 0.5.4. For 0.5.4 or later, use the current tutorials.

The same workflow as cMD: paracetamol, for a second small molecule: Chinolin, C₉H₇N — quinoline in English. It is here to show that nothing in the steps is specific to one molecule: only the SMILES line changes. Run with md-tools 0.5.3; every number is copied from that run (one NVIDIA RTX 3080, CUDA, mixed precision).

If you have not done the paracetamol tutorial, read it first; this page does not repeat its explanations.

1. Inputs

mkdir -p CHINOLIN/build
cd CHINOLIN/build

chinolin.smi:

c1ccc2ncccc2c1 chinolin

build-top.config:

solute:
  kind: ligand

2. Build

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

Input interpretation
  interpreted as              single-molecule SMILES
  smiles                      c1ccc2ncccc2c1
  small-molecule FF           sage-2.2.1
  solvent treatment           explicit TIP3P, periodic
Preparation
  protonation  : pH 7.0, 7 -> 7 hydrogens
Counts
  atoms                       1806
  solute atoms                17
  waters                      595
  ions                        {'NA': 2, 'CL': 2}
Summary
  status: completed

7 -> 7 hydrogens: the ring nitrogen is left unprotonated at pH 7 (the conjugate acid's pKa is about 4.9), so the molecule is neutral — 9 carbons, 1 nitrogen and 7 hydrogens, 17 atoms.

3. Generate and run

cMD.config at the dataset root is identical to the paracetamol one:

protocol: cMD
solvent: explicit

stages:
  minimization_iterations: 1000
  restrained_nvt_steps: 5000
  restrained_npt_steps: 5000
  unrestrained_npt_steps: 5000
  production_steps: 100000

reporting:
  crd_printout_solute: 500
  info_printout: 5000
  checkpoint_printout: 5000

cd ..                                            # CHINOLIN/
md-openmm build-md -odir ./cMD-run1 --config cMD.config
cd cMD-run1
./run.sh

== min ==
== eq_1 ==
== eq_2 ==
== eq_3 ==
== cMD ==
...
  cMD: 100000 steps completed, 200 ps
  status: completed
run.sh: all stages reported completion

The whole chain took 36 s.

4. Result

From cMD-run1/cMD.out:

System
  residues                     600 (HOH 595, CL 2, NA 2, UNL 1)
Averages
  Temperature (K)              mean 298.616   rms fluctuation 5.13951
  Density (g/mL)               mean 0.99185   rms fluctuation 0.00689213
  Speed (ns/day)               mean 1245.2   rms fluctuation 312.025

The outputs have the same names and meanings as in the paracetamol tutorial: solute_prod1.nc is the trajectory, mdout.csv the state table, cMD.xml the final state, and cMD.log the record completion is read from.