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Desmond Molecular Dynamics

DeprecatedDeprecated Nodes version 21.1.156.202102141445 by Schrödinger

Molecular dynamics jobs simulate the Newtonian dynamics of the model system, producing a trajectory of the particles, coordinates, velocities, and energies, on which statistical analysis can be performed to derive properties of interest about the model system. The molecular dynamics task performs a single MD simulation under the chosen ensemble condition for a given model system, generating simulation data for post-simulation analysis. The Molecular Dynamics panel is designed to make setting up jobs as easy as possible. The main panel provides the most common simulation controls, while the Advanced Options dialog box provides access to a larger range of parameters. The default values represent a good balance between accuracy and performance and work for most jobs without change, but can be changed as needed.

Platform Limitations: Linux only

Backend implementation

scripts/write_desmond_configFILE.py creates a config file based on the settings from the dialog.
utilities/multisim carries out the molecular dynamics job

Options

Column containing input model system
Column in the input data table containing the input model systems. If a Desmond Trajectory column is selected, then the corresponding CMS file will be loaded.
Output Column Structure
Choose the output columns:

Input plus Output - The input columns are included in the output.

Output replaces Input - The output columns are the same as the input, with the output structures replacing the input column selected

Output only - Only Output structures

Location of output files
If selected, this is where the output trajectory directory will be stored, otherwise it will be kept in the temporary directory (not recommended).
Change base name of files
The output files will start with this name, if selected. Existing files will be overwritten.
Simulation time
Specify the total time of the simulation.
Recording interval-energy
Specify the recording period for the energy.
Recording interval-trajectory
Specify the recording period for the trajectory.
Ensemble class
Select the ensemble class from the five available classes: NVE, NVT, NPT, NPAT, and NPγT
Temperature
Specify the temperature to be used, in kelvin. Not available for the NVE ensemble class.
Pressure
Specify the pressure to be used. Not available for the NVE and NVT ensemble classes.
Surface tension
Specify the surface tension to be used. Only available for the NPγT ensemble class.
Relax model system before simulation
When selected, a series of minimizations and short molecular dynamics simulations are performed to relax the model system before performing the simulation you set up. Normally, this option is needed only for model systems that have just been prepared with the System Builder panel and have not been relaxed. This option is selected by default.
Relaxation protocol
This text box specifies the protocol to be used for the relaxation. When the panel is opened, the text box contains the text Use default protocol, indicating that the default is in effect. You can select your own protocol by clicking Browse and selecting the appropriate .msj file for the relaxation. The text box then shows the name of the file you selected.
RESPA integrator
Specify the time steps in fs for bonded, near, and far, by entering values in the text boxes, or using the arrow buttons. Because the bonded, near, and far time steps must maintain a certain ratio, when a new value is set for the bonded time step, the other two time steps are automatically updated according the current ratio. Changing the near or far time steps adjusts this ratio.
Thermostat method
Select the thermostat method from the option menu, from Nose-Hoover, Berendsen, Langevin, or None. The thermostat method and the barostat method are coupled: the choice you make from the Thermostat method option menu changes the selection from the Barostat method option menu. The exception is that you can choose None for the barostat method for any of the thermostat methods.
Thermostat relaxation time
Enter the relaxation time for the thermostat method.
Barostat method
Select the barostat method from the option menu, from Martyna-Tobias-Klein, Berendsen, or None. The thermostat method and the barostat method are coupled: the choice you make from the Barostat method option menu changes the selection from the Thermostat method option menu. The exception is that you can choose None for the barostat method for any of the thermostat methods.
Barostat relaxation time
Enter the relaxation time in ps in this text box.
Barostat coupling style
Choose the coupling style from this option menu, from Isotropic, Semi-isotropic, Anisotropic, and Constant area.
Short range method
Choose the method for defining the short-range region from this option menu, from Cutoff, Force tapering, or Potential tapering. The controls below this menu depend on the method chosen.
Cutoff radius
Specify the cutoff radius for the Cutoff method.
Tapering range
Specify the range in angstroms over which the force or the potential is tapered off in the two text boxes.
Long range method
Choose the method for handling the long-range Coulombic interactions. The choices are Smooth particle mesh Ewald, and None.
Ewald tolerance
Specify the tolerance for the Ewald method. This tolerance affects the accuracy of the long-range Coulombic interactions. The smaller the tolerance is, the more accurate the computation of the long-range Coulombic interactions is, but the simulation will be correspondingly slower.
Position restraints
Lists the restraints. You must enter the force constant for the restraint in the Force Constant column and an ASL expression for the atoms. Selecting the add button will add a row to the restraints table.
Energy sequence file
This file contains a sequence of various energies of the system.
Energy recording starting time
Trajectory directory
This directory is used by Desmond to periodically write out files to record coordinates and velocities (optional) of all particles in the system at a particular point in the simulation. You can provide a title for the trajectory.
Trajectory recording starting
Record velocities
Select this option if you want the velocities to be recorded along with the coordinates.
Glue close solute molecules together
To ensure that associated solutes appear together rather than on opposite sides of the simulation box, you can select this option however it only affects the way the trajectory is displayed.
Checkpoint file
his file contains information that can be used to restart an interrupted simulation.
Checkpoint recording starting time
Checkpoint recording interval
Randomize velocities starting time
Randomize velocities interval

Input Ports

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Model system in CMS or Trajectory format

Output Ports

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Trajectory format

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Installation

To use this node in KNIME, install Schrödinger Extensions for KNIME from the following update site:

KNIME 4.3

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