# mm

Classical molecular mechanics (MM) calculation.

The MM system is specified by a structure (provided through the usual structure command) and further options to specify the force field.

To run a force field through OpenMM, specify an XML file representing an OpenMM System object.

As a top-level command, this calculates the classical MM potential energy of the given atomic structure.

This command can appear in the global context.

### Options

constraint_tol

Tolerance within which distance constraints should be satisfied, as a fraction of constrained distance.

This only has an effect when performing MD with OpenMM and when constrained distances are specified in the System XML file.

Note: OpenMM automatically selects the appropriate constraint method for constraints specified in the System and this may affect how the tolerance is applied to individual constraints. For example, the constraint tolerance will have no effect for constraints that can be applied using the analytic SETTLE algorithm (e.g. for rigid TIP3P water molecules).

• The type is real
• The default is 1e-5
• The value must be nonnegative
force_field

Specify a force field by name.

• The type is string-lowered
• There is no default value.
• The value must be one of:
name

Specify the name of a set of results.

This option is deprecated.

• The type is string
• There is no default value.
platform

Name of OpenMM platform to use, e.g. Reference, CPU. If this is not specified, OpenMM will automatically select the platform to use.

For production calculations, it is recommended to set this variable to a suitable platform for your environment to ensure that you are obtain consistent results (there is some variation between platforms).

See the OpenMM user guide for details of the platforms available.

• The type is string
• There is no default value.
print_level

Print level.

• The type is int
• There is no default value.
• The value must be one of:
• -2 - No output
• -1 - Minimum output
• 0 - Output that doesn't scale with system size
• 1 - Output that scales linearly with system size
• 2 - (Debugging) output that scales quadratically with system size
• 3 - (Debugging) output that scales cubically with system size
system

Filepath of an OpenMM XML file to be used to set up the molecular mechanics system. This should contain the XML representation of an OpenMM System object. An OpenMM System contains information about the set of particles in the system and their interactions (forces, constraints), but not the spatial arrangement of particles.

A tool for generating System XML and structure inputs for MM calculations from PDB and OpenMM forcefield XML files is distributed with entos (in the tools/mm/ directory).

A System XML file can also be prepared directly from an existing OpenMM System object using the XmlSerializer class in the C++ and Python APIs.

• The type is string
• There is no default value.
use_constraints

Specify whether to apply distance constraints to positions and velocities during integrator steps.

This only has an effect when performing MD with OpenMM and when constrained distances are specified in the System XML file.

• The type is bool
• The default is true