Easy to deploy MD protocols for OpenMM
By Jaime Rodríguez-Guerra (@jaimergp)
Contributors: Lur Alonso, Patricia Saura
Really easy with Conda. If you don't know what Conda is, check its webpage. Quick steps:
-
Download and install Miniconda.
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh bash Miniconda3*.sh -
Restart terminal and add
omniaandinsilichemto the channels list.conda config --add channels omnia conda config --add channels insilichem -
Install ommprotocol in an environment called
openmm:conda create -n openmm ommprotocol -
Activate the environment
source activate ommprotocol -
Test
ommprotocol -h
Quick help:
ommprotocol -h
Input file (last argument, no flags) can be:
- Standard PDB (topology and coordinates). Protocol MUST include OpenMM forcefields to use.
- Amber's PRMTOP (topology and forcefields).
- Charmm PSF with accompanying topology. Protocol MUST include parameters files in
charmm_parameters.
Additional inputs:
- Amber's inpcrd or Namd's coor for input coordinates (
-c). Required for PRMTOP and PSF. - Namd's vel for velocities (
-v). - Charmm .restart (used by this script) to restore positions and velocities (
-r). - Protocol file (
-p). This file can specify forcefields, Charmm parameters, and finally, the MD system options and stages.
Some example protocols ready to use are present in folder data/. Use them as examples.
Protocols use a YAML file with at least one entry called stages.
This entry is a list of dictionaries, each specifying the options for that stage.
See example.yaml for completeness.
The YAML file can also contain another top-level entry called system,
specifying the global options for the system creation (non bonded methods, etc).
Additionally, the protocol can include different forcefields than default ones (amber99sbildn, tip3p)
with key forcefields. For example:
forcefields:
- amber10.xml
- tip3p.xml
If you are using a PSF file as input, then it MUST contain a key charmm_parameters
with the list of charmm parameters to load. It can be empty ([]), but it must be present. For example:
charmm_parameters:
- top.par
- system.str
These are the same as OpenMM default values. Just for quick reference:
| Variable | System key | Default | Other values | Comments |
|---|---|---|---|---|
| Non bonded method | nonbondedMethod |
NoCutoff | CutoffNonPeriodic, CutoffPeriodic, Ewald, PME | OpenMM docs |
| Non bonded cutoff (nm) | nonbondedCutoff |
1.0 | ||
| Constraints | constraints |
None | HBonds, AllBonds, HAngles | OpenMM docs |
| Water rigidity | rigidWater |
True | False | |
| Remove center of mass motion | removeCMMotion |
True | False | |
| Mass of hydrogen atoms | hydrogenMass |
None | The mass to use for hydrogen atoms bound to heavy atoms. Any mass added to a hydrogen is subtracted from the heavy atom to keep their total mass the same |
| Variable | Stage key | Default | Other values | Comments |
|---|---|---|---|---|
| Forcefields | forcefield |
amber99sbildn, tip3p | Check OpenMM forcefields | Only applies if the input is a PDB file |
| Timestep (fs) | timestep |
1.0 | ||
| Temperature (K) | temperature |
300 | ||
| Barostat | barostat |
True | False | |
| Barostat pressure (bar) | _pressure |
1.01325 | ||
| Simulation steps | md_steps |
0 | ||
| Restraints on atoms | restrained_atoms |
None | backbone, protein, protein_no_H | A force is applied on selected atoms to largely reduce movement. |
| Restraint strength (kJ/mol) | _restraint_strength |
5.0 | ||
| Constraints on atoms | constrained_atoms |
None | backbone, protein, protein_no_H | Selected atoms won't move at all |
| Minimize structure | minimize |
True | False | |
| Trajectory output format | trajectory |
None | DCD, PDB, HDF5 | |
| Trajectory output frequency | trajectory_step |
10000 | ||
| Console output frequency | stdout_step |
1000 | 0 to disable | |
| Restart output frequency | restart_step |
1000000 | 0 to disable | |
| Output folder | output |
. | Relative to working directory | |
| Protocol name output files | project_name |
random string | The same for all stages | |
| Stage name | name |
random string | Stage dependent | |
| Integrator | _integrator |
LangevinIntegrator | BrownianIntegrator, CustomIntegrator, DrudeLangevinIntegrator, DrudeSCFIntegrator, LangevinIntegrator, RPMDIntegrator, VariableLangevinIntegrator, VariableVerletIntegrator, VerletIntegrator | OpenMM docs |
| Integrator friction (1/ps) | _friction |
1.0 | ||
| Override system defaults | _system_kwargs |
Global ones | Check System defaults section and [1] |
[1] System options can be also specified for each stage independently with _system_kwargs,
updating the global options. This means that a per-stage system options will take
precedence over the global system options in case of key conflict. If you already
defined these global options:
system: {a: 0, b: 1}
and then in a stage you specify:
_system_kwargs: {a: 1, c: 2}
The resulting options would be:
system: {a:1, b: 1, c:2}