Quick usage¶
OMMProtocol¶
Once installed (Installation & Updates), first thing to do is creating the input file (OMMProtocol input files) for your simulation. This task usually involve two different steps:
- Getting the structural data (topology, coordinates)
- Specifying the simulation details:
- Forcefield parameters
- Solvation conditions: explicit, implicit, no solvent?
- Simulation conditions: temperature, pressure, NPT, NVT?
- Technical details: how to compute non-bonded interactions, whether to use periodic boundary conditions, whether to constrain some specific types of bonds, the integration method and timestep…
These details are probably out of the scope of this documentation, and the reader is encouraged to read specific tutorials about this, such as:
With a correctly formed YAML input file named, for example, simulation.yaml, the user can now run:
ommprotocol simulation.yaml
If the structure is correctly formed and the forcefield parameters are well defined, the screen will now display a status like this:
The generated files will be written to the directory specified in the outputpath
key (or, if omitted, to the same directory simulation.yaml is in), with the following name format: [globalname]_[stagename].[extension]
, where globalname
is the value of the global name
key in the input file, and stagename
is the value of the stage
key in each stage.
Most of this files can be opened during the simulation. That way you can check the progress of the trajectory in viewers like VMD, PyMol or UCSF Chimera. Since .log files are created by default with some metadata about the simulation (temperature, potential energy, volume…), they are a convenient way of checking if everything is working OK. For example, the energies and temperatures should be more or less constant. To do that, a helper utility called ommanalyze
is included, which is able to produce interactive plots of such properties:
OMMAnalyze¶
ommanalyze
is a small collection of analysis utilities for topologies and trajectories. Currently, it offers three subcommands:
ommanalyze log
: Plot *.log reports generated by OMMProtocol (energies, temperature, volume…).ommanalyze rmsd
: Performs RMSD analysis on trajectories. Produces plots and plain-text file. Since it uses MDTrajiterload
, it does not load all the files at once and allows you to analyze long trajectories with small memory footprint.ommanalyze top
: Quick summary of any topology supported by MDTraj. Designed to debug subset selection queries with--subset
flag. Checkmdinspect
(provided by MDTraj) for more advanced debugging.
Examples¶
> ommanalyze rmsd -t my_topology.prmtop -s 'backbone' my_trajectories*.dcd
0%| | 0/26 [00:00<?, ?file/s]
40%|█████▏ | 200/500 [00:02<00:03, 77.95frames/s, traj=my_trajectories_01.dcd]
> ommanalyze top my_topology.prmtop -s 'resname UNK'
Topology my_topology.prmtop
***
Contents:
- 1 chains
- 39956 residues
- 132199 atoms
- 132463 bonds
***
Subset `resname UNK` will select 13 atoms.
name element resSeq resName chainID segmentID
14550 H160 H 887 UNK 0
14551 C145 C 887 UNK 0
14552 H159 H 887 UNK 0
14553 C144 C 887 UNK 0
14554 H157 H 887 UNK 0
14555 H158 H 887 UNK 0
14556 N30 N 887 UNK 0
14557 C143 C 887 UNK 0
14558 H156 H 887 UNK 0
14559 C142 C 887 UNK 0
14560 C141 C 887 UNK 0
14561 H154 H 887 UNK 0
14562 H155 H 887 UNK 0
14563 O66 O 887 UNK 0