docs/yamlpages/cookbook.rst
.. _yaml_cookbook_head:
Cookbook for YAML Options
*************************
Having all the options laid out in front of you is good for advanced users, but sometimes practical examples are much more helpful.
Below is the YANK YAML Cookbook:
A series of examples that may help you understanding how to put together the options found on the other pages.
----
Best Practices Shown by These Examples
======================================
The following examples exemplify some of the `best practices <http://www.alchemistry.org/wiki/Best_Practices>`_ laid out on
`alchemistry.org <http://www.alchemistry.org/>`_. Specifically:
* There are no partial atomic charges on an atom while its Lennard-Jones interactions are being removed.
* The whole free energy setup and run is automated through YANK's YAML format, meaning its easily transferable and repeatable
* A statistically efficient alchemical path is selected because the ``softcore_X`` parameters were not set, so the default,
efficient, soft core parameters were chosen automatically.
.. _yaml_ex_implicit:
Example: Implicit Solvent Binding Simulation:
=============================================
This example sets up para-xylene binding to T4-Lysozyme in implicit solvent.
We recommend these settings as a good baseline simulation setup.
Although you do not have to set all these options (e.g. the ligand may be a pdb file, not just a SMILES string), many
of these options are good stock settings to remember.
In this example:
* Targeting folders for input files
* Configuring Output files
* Setting good stock options for implicit simulations
* Setting up simple protein/ligand binding simulation
* NVT ensemble
.. code-block:: yaml
options:
verbose: yes
setup_dir: setup
output_dir: output
experiments_dir: experiments
randomize_ligand: yes
minimize: yes
default_number_of_iterations: 2000
temperature: 300*kelvin
pressure: null
molecules:
T4_lysozyme:
filepath: T4.pdb
p-xylene:
smiles: CC1=CC=C(C=C1)C
antechamber:
charge_method: bcc
solvents:
GBSA:
nonbonded_method: NoCutoff
implicit_solvent: OBC2
solvent_dielectric: 78.5
systems:
T4-xylene-complex:
receptor: T4_lysozyme
ligand: p-xylene
solvent: GBSA
pack: yes
leap:
parameters: [leaprc.ff14SB, leaprc.gaff]
protocols:
absolute-binding:
complex:
alchemical_path:
lambda_electrostatics: [1.00, 0.95, 0.90, 0.85, 0.80, 0.75, 0.70, 0.65, 0.60, 0.55, 0.50, 0.45, 0.40, 0.35, 0.30, 0.25, 0.20, 0.15, 0.10, 0.05, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00]
lambda_sterics: [1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 0.95, 0.90, 0.85, 0.80, 0.75, 0.70, 0.65, 0.60, 0.55, 0.50, 0.45, 0.40, 0.35, 0.30, 0.25, 0.20, 0.15, 0.10, 0.00]
solvent:
alchemical_path:
lambda_electrostatics: [1.00, 0.95, 0.90, 0.85, 0.80, 0.75, 0.70, 0.65, 0.60, 0.55, 0.50, 0.45, 0.40, 0.35, 0.30, 0.25, 0.20, 0.15, 0.10, 0.05, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00]
lambda_sterics: [1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 0.95, 0.90, 0.85, 0.80, 0.75, 0.70, 0.65, 0.60, 0.55, 0.50, 0.45, 0.40, 0.35, 0.30, 0.25, 0.20, 0.15, 0.10, 0.00]
experiments:
system: T4-xylene-complex
protocol: absolute-binding
restraint:
type: FlatBottom
After this is all setup, simply run: ``yank script --yaml={ThisScriptName.yaml}`` and YANK will take care of the rest for you.
----
.. _yaml_ex_explicit:
Example: Absolute Binding free energy in explicit solvent
=========================================================
This example takes the same para-xylene binding to T4-Lysozyme system as before, but now uses an explicit solvent setup,
minimal options, and automatic water addition (TIP3P).
This example also shows how to make YANK run with MPI; assumes 4 nodes are available.
It should be noted there is nothing you set in the YAML file or with YANK itself to run with MPI.
YANK automatically detects if MPI was called to run YANK and interacts with it accordingly.
In this Example:
* Automatic solvent addition
* Setting good stock options for explicit simulations
* Call MPI
* NPT ensemble
.. code-block:: yaml
options:
minimize: yes
verbose: yes
output_dir: .
default_number_of_iterations: 2000
temperature: 300*kelvin
pressure: 1*atmosphere
molecules:
t4-lysozyme:
filepath: setup/receptor.pdbfixer.pdb
parameters: leaprc.ff14SB
p-xylene:
filepath: setup/ligand.tripos.mol2
antechamber:
charge_method: bcc
solvents:
PME:
nonbonded_method: PME
nonbonded_cutoff: 0.9*nanometer
switch_distance: 0.8*nanometer
clearance: 12*angstroms
positive_ion: Na+
negative_ion: Cl-
systems:
t4-xylene-explicit:
receptor: t4-lysozyne
ligand: p-xylene
solvent: PME
leap:
parameters: [leaprc.ff12, leaprc.gaff]
protocols:
absolute-binding:
complex:
alchemical_path:
lambda_electrostatics: [1.00, 0.95, 0.90, 0.85, 0.80, 0.75, 0.70, 0.65, 0.60, 0.55, 0.50, 0.45, 0.40, 0.35, 0.30, 0.25, 0.20, 0.15, 0.10, 0.05, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00]
lambda_sterics: [1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 0.95, 0.90, 0.85, 0.80, 0.75, 0.70, 0.65, 0.60, 0.55, 0.50, 0.45, 0.40, 0.35, 0.30, 0.25, 0.20, 0.15, 0.10, 0.00]
solvent:
alchemical_path:
lambda_electrostatics: [1.00, 0.95, 0.90, 0.85, 0.80, 0.75, 0.70, 0.65, 0.60, 0.55, 0.50, 0.45, 0.40, 0.35, 0.30, 0.25, 0.20, 0.15, 0.10, 0.05, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00]
lambda_sterics: [1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 0.95, 0.90, 0.85, 0.80, 0.75, 0.70, 0.65, 0.60, 0.55, 0.50, 0.45, 0.40, 0.35, 0.30, 0.25, 0.20, 0.15, 0.10, 0.00]
experiments:
system: t4-xylene-explicit
protocol: absolute-binding
restraint:
type: Harmonic
Now run:
.. code-block:: bash
$ build_mpirun_configfile "yank script --yaml=yank.yaml"
$ mpiexec -f hostfile -configfile configfile
The ``build_mpirun_configfile`` is a command available if you have installed YANK through conda, and though the ``clusterutils``
repo.
.. .. _yaml_raw_examples:
Raw YAML File Examples
======================
.. literalinclude:: ../yank-yaml-cookbook/all-options.yaml
:language: yaml
|
.. literalinclude:: ../yank-yaml-cookbook/combinatorial-experiment.yaml
:language: yaml