Examples

Examples for running KIMMDY with different options for various systems

Further Examples

KIMMDY contains examples generated from our internal test systems. Those examples don’t currently have extensive documentation, but they can be used as a starting point for your own simulations.

The examples are located in the examples directory of the KIMMDY source code here.

Here are their kimmdy.yml files at a glance:

hexalanine_homolysis

dryrun: false
name: 'hexalanine_homolysis_000'
gromacs_alias: 'gmx'
gmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1
ff: 'amber99sb-star-ildnp.ff'
top: 'hexala_out.top'
gro: 'npt.gro'
ndx: 'index.ndx'
plumed: 'plumed.dat'
mds:
  equilibrium:
    mdp: 'md.mdp'
  pull:
    mdp: 'md.mdp'
    use_plumed: true
  relax:
    mdp: 'md_slow_growth.mdp'
changer:
  coordinates:
    md: 'relax'
    slow_growth: True
  topology:
    parameterization: 'basic' 
reactions:
  homolysis:
    edis: 'edissoc.dat'
    itp: 'ffbonded.itp'
sequence:
  - equilibrium
  - pull  
  - reactions
  - equilibrium
  - pull

alanine_hat_naive

dryrun: false
name: 'alanine_hat_000'
gromacs_alias: 'gmx'
gmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1
ff: 'amber99sb-star-ildnp.ff' # optional, dir endinng with .ff by default 
top: 'Ala_out.top'
gro: 'npt.gro'
ndx: 'index.ndx'
kmc: "rfkmc"
mds:
  equilibrium:
    mdp: 'md.mdp'
  relax:
    mdp: 'md_slow_growth.mdp'
changer:
  coordinates:
    md: 'relax'  
    slow_growth: True
  topology:
    parameterization: 'basic'
reactions:
  hat_naive:
    frequency_factor: 100000000
    h_cutoff: 3
    polling_rate: 1

sequence:
- equilibrium
- mult: 2
  tasks:
  - equilibrium
  - reactions

triplehelix_pull

name: 'kimmdy_001'
dryrun: false
gromacs_alias: 'gmx'
gmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1
ff: 'amber99sb-star-ildnp.ff' # optional, dir endinng with .ff by default 
top: 'topol.top'
gro: 'npt.gro'
ndx: 'index_backbone.ndx'
plumed: 'plumed.dat'
mds:
  equilibrium:
    mdp: 'pullf1500_equil.mdp'
  prod:
    mdp: 'pullf1500.mdp'
    use_plumed: true
  relax:
    mdp: 'pullf1500_slow_growth.mdp'
changer:
  coordinates:
    md: 'relax'
    slow_growth: true
  topology:
    parameterization: 'basic' 
    parameterization_kwargs: 
      arg1: hello
      arg2: 1
reactions:
  homolysis:
    edis: 'edissoc.dat'
    itp: 'ffbonded.itp'
sequence:
  - equilibrium
  - mult: 1
    tasks:
      - prod
      - reactions
  - equilibrium

hexalanine_single_reaction

dryrun: false
name: 'single_reaction_000'
gmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1
ff: 'amber99sb-star-ildnp.ff'
top: 'hexala_out.top'
gro: 'npt.gro'
ndx: 'index.ndx'
plumed: 'plumed.dat'
trr: 'pull.trr'
changer:
  coordinates: {}
  topology:
    parameterization: 'basic' 
reactions:
  homolysis:
    edis: 'edissoc.dat'
    itp: 'ffbonded.itp'
  dummyreaction: {}
sequence:
  - homolysis

charged_peptide_homolysis_hat_naive

name: 'kimmdy_001'
dryrun: false
gromacs_alias: 'gmx'
gmx_mdrun_flags: -maxh 24 -dlb yes -nt 8
top: 'IMREE.top'
gro: 'IMREE_npt.gro'
ndx: 'index.ndx'
kmc: rfkmc
plumed: 'plumed.dat'
mds:
  equilibrium:
    mdp: 'md.mdp'
  pull:
    mdp: 'md.mdp'
    use_plumed: true
  relax:
    mdp: 'md_slow_growth.mdp'
changer:
  coordinates:
    md: 'relax'    
    slow_growth: True
  topology:
    parameterization: 'grappa' 
reactions:
  homolysis:
    edis: 'edissoc.dat'
    itp: 'ffbonded.itp'
  hat_naive:
    frequency_factor: 100000000
    h_cutoff: 3
    polling_rate: 1
plot_rates: true
save_recipes: true
sequence:
  - equilibrium
  - pull
  - homolysis
  -
    mult: 2
    tasks:
      - equilibrium
      - pull
      - reactions