Command-line reference

fastmdx explore --system 1UBQ --output runs/study

That is the shape of it: a command, a structure, somewhere to put the results.

The commands


`fastmdx explore`	all four phases
`fastmdx setup`	prepare a system and stop
`fastmdx simulate`	run dynamics on a prepared system
`fastmdx analyze`	measure a trajectory
`fastmdx report`	write up an existing run
`fastmdx gui`	the GUI
`fastmdx info`	what is installed, and how to get what is not
`fastmdx init-config`	write a commented config template

How the flags are named

Every setting belongs to a phase, and its flag is the phase and the setting:

--{phase}-{setting}

So setup.ph is --setup-ph, simulation.timestep_fs is --simulate-timestep-fs, report.pdf is --report-pdf (and --report-no-pdf to turn it off).

That is not a convention somebody maintains — the flags are generated from the same declaration the config file and the GUI are built from, so a setting that exists has a flag, and a flag that exists does something.

The authoritative list is --help:

fastmdx explore --help          # every flag, with what it does
fastmdx simulate --help         # just the simulation ones

It is generated, so it is never out of date. This page covers the ones you will reach for.

Input and output

--system 1UBQ                   # a PDB identifier
--system protein.pdb            # or a file
--output runs/study             # where everything goes
--config study.yml              # or take it all from a file

The form of --system is detected, so there is no separate flag for a PDB identifier.

Running part of it

fastmdx explore --system 1UBQ --output runs/study \
  --include setup simulation          # stop after the trajectory

fastmdx analyze \
  --trajectory production.dcd \
  --topology system.pdb \
  --output runs/analysis              # measure something you already have

A first run that finishes quickly

The defaults are a real simulation. For checking the machinery:

fastmdx explore --system 1L2Y --output runs/smoke \
  --simulate-nvt-steps 500 \
  --simulate-npt-steps 500 \
  --simulate-production-steps 5000 \
  --simulate-trajectory-interval-steps 50

Ten picoseconds, which the report will tell you supports nothing.

The flags you will actually use

How long

--simulate-duration-ns 100            # or the three step counts separately
--simulate-timestep-fs 2.0

Conditions

--simulate-temperature-K 310
--setup-ph 7.0
--setup-ion-concentration-M 0.15

Force field

--setup-forcefield amber14            # protein only
--setup-forcefield amber-openff       # and a ligand

Which analyses

--analyze-analyses rmsd rmsf ss       # only these
--analyze-exclude-analyses sasa       # everything but

Where it runs

--simulate-platform CUDA
--simulate-device-index 0
--simulate-precision mixed

Enhanced sampling, membranes, restraints — see Beyond a box of water.

Checking things

fastmdx --version
fastmdx info                          # backends, and what to install
fastmdx explore --config study.yml --dry-run   # validate without running