Running MxMD Simulations from the Command Line

An MxMD simulation is launched from the command line with the mxmd program.

To run MxMD simulations in Maestro instead, see Mixed Solvent MD Panel

Running MxMD Simulations

See Preparing solutes for how to prepare the input structure.

Submit the MxMD simulation on the command line:

$SCHRODINGER/mxmd input_structure.mae -HOST cpu_host SUBHOST <gpu_host> -JOBNAME mxmd_job

By default, acetonitrile, isopropanol, and pyrimidine are used as cosolvent probes. For each probe, 10 simulations will be performed with different starting conditions, resulting in 30 independent simulations of 20 ns length and a total simulation time of 600 ns.

If you are running MxMD on a membrane protein, use the -membrane option. See System Setup for Membrane Proteins for procedure details. For example, to specify a POPC bilayer:

$SCHRODINGER/mxmd input_structure.mae -membrane POPC -HOST cpu_host SUBHOST <gpu_host> -JOBNAME mxmd_job

Some useful options include:

-ff {OPLS4|OPLS5}

Specify the forcefield to use. (Default: OPLS4)

-time <real>

Specify time (in ps) for the production simulation stage. (Default: 5000.0)

-time-equilibrate <real>

Specify time (in ps) for the equilibration simulation stage. (Default: 15000.0)

-probe <string>

Specify the cosolvent probes. Default: acetonitrile,isopropanol,pyrimidine; See MxMD Cosolvent Probes for the full list of supported probes.

-membrane MEMBRANE

Build a membrane-containing system, and use membrane-specific MD protocol to run subjobs. If this option is used, the receptor orientation reference should be OPM-compatible. Available membrane bilayers are: DPPC, POPE, DMPC, and POPC. (Default: None)

-init-water-buffer <real>

Specify a guess for the initial water box buffer. The box will then be shrunk to match the volume/volume ratio. (Default: 17.0)

-nsim-per-probe <integer>

Specify number of simulations per probe. Default: 10

-custom-probe-dir CUSTOM_PROBE_DIR

Specify custom probe directory. There must be a <probe_name>.box.mae file in this directory for each custom probe passed in using -custom-probe-dir. See MxMD Custom Cosolvent Probes for more information about preparing custom cosolvent probes. (Default: No custom probe directory)

See mxmd Command Help for a complete list of options.

Customizing MxMD Parameters and Water Model

You can modify the MxMD workflow by using the -prepare option of mxmd. This option writes two multisim job files: mxmd_job.msj and mxmd_job_md.msj. If you want to modify the relaxation protocol, edit the file mxmd_job_md.msj. If you want to use a different water model, or change other parameters of the MxMD simulation, edit the file mxmd_job.msj. To use the modified .msj files instead of the default ones, use the -m option of mxmd.