Preparing Desmond Systems

Building a Desmond Model System

Generally, multisim can be used to build a Desmond model system by creating a workflow consisting of a build_geometry stage followed by an assign_forcefield stage.

An example workflow to build a model system looks like this:

task {
  task = "desmond:auto"
}

build_geometry {
  add_counterion = {
    ion = Cl
    number = neutralize_system
  }
  box = {
    shape = orthorhombic
    size = [10.0 10.0 10.0]
    size_type = buffer
  }
  override_forcefield = OPLS4
  rezero_system = false
  salt = {
    concentration = 0.15
    negative_ion = Cl
    positive_ion = Na
  }
  solvent = SPC
}

assign_forcefield { 
  forcefield = OPLS4
}

This example adds an orthorhombic box around the solute with a minimum distance of 10 Å between the solute and the edge of the box. To neutralize the system, chloride ions are added. In addition, Na and Cl ions are added to simulate a salt concentration of 0.15 mol⋅L^-1. The force field, OPLS4, is specifying the OPLS4 force field.

See The build_geometry Stage and The assign_forcefield Stage topics for more information.

If you want to rebuild a model system from the command line, you should run one job from Maestro, and then edit the multisim input file (.msj) for other model systems.

Preparing a Custom Solvent Box

If you want to use a solvent other than the ones that are available in the installation, you can create a solvent box for input to the system builder. The solvent molecule must be supplied in a Maestro file. The commands to run are:

$SCHRODINGER/utilities/multisim -JOBNAME jobname -HOST hostname -maxjob 1 -cpu 1 -mode umbrella \
	-m $SCHRODINGER/mmshare-v7.3/data/desmond/mxmd_cosolvent_probe_generation.msj solvent.mae
$SCHRODINGER/run -FROM desmond generate_solvent_box.py jobname_probe-out.cms output-basename -t jobname_probe.xtc -s "start:end:step"

The -s option specifies the frames in the trajectory to extract into the output structure file that is used as the solvent box. For use as a Desmond solvent, there must be only one frame specified. The notation is the Python notation for a slice. This procedure is also used to generate cosolvents for MxMD—see MxMD Custom Cosolvent Probes for more information.