Desmond — Advanced Options Dialog Box

This dialog box provides access to advanced options for control of the simulation or the minimization, such as the frequency of data output, integration time step sizes, thermostat and barostat parameters, restraints, cutoff radii, and so on. The dialog box title includes the name of the parent panel, e.g. Metadynamics - Advanced Options.

The settings in this dialog box and the settings in the Desmond panel are not entirely independent, and can affect each other. For example, changing the far time step can affect the values of the recording periods in the panel, because the latter are automatically rounded by the far time step. As another example, changing the temperature or pressure in the Desmond panel updates the temperature or pressure parameters in the dialog box. Changes in the Desmond panel take effect immediately and update parameters in the dialog box, whereas changes made in the dialog box only take effect when you click OK or Apply.

Features
Additional Resources

Advanced Options Dialog Box Features

Integration tab
- RESPA integrator section
Ensemble tab
- Thermostat section
  - Thermostat method option menu
  - Relaxation time text box
- Barostat section
Interaction tab
- Coulombic section
- Scaled Effective Solvent scaling factor text box
Restraints tab
Output tab
Misc tab
Reset button

The selection of tabs available depends on the task.

Integration tab

Set parameters for the integration algorithm. This tab has one section:

RESPA integrator section: Specify the time steps in fs for bonded, near, and far, by entering values in the text boxes, or using the arrow buttons to change the value in increments of the bonded time step. 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.

Ensemble tab

In this tab you can set the thermostat method and the barostat method and make settings for these methods. There are two sections:

Thermostat section

Make settings for the thermostat in this section.

Thermostat method option menu

Select the thermostat method from the option menu, from Nose-Hoover chain, Langevin, DPD or None. The DPD (dissipative particle dynamics) method is available with the NVT and NPT ensembles, and should only be used for coarse-grained modeling jobs run on a GPU.

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 exceptions are that you can choose None for the barostat method for any of the thermostat methods, and the Langevin barostat is the only one available with the DPD thermostat method.

Relaxation time text box

Enter the relaxation time in ps for the thermostats. For the Langevin thermostat, an appropriate value is 0.02.

Barostat section

The controls for the barostat method are:

Barostat method option menu: Select the barostat method, from Martyna-Tobias-Klein, Langevin, 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. The Langevin barostat is the only one available with the DPD thermostat method.
Relaxation time text box: Enter the relaxation time in ps in this text box.
Coupling style option menu: Choose the coupling style from this option menu, from Isotropic, Semi-isotropic, Anisotropic, Constant area, and Flexible-angle. The flexible-angle coupling allows the lattice angles of the unit cell to change during the simulation, and is only available with the Martyna-Tobias-Klein barostat, when setting up the simulation in the MD Multistage Workflow Panel.

Interaction tab

In this tab you can specify how interactions are handled.

Coulombic section

Specify how the short-range and long-range Coulombic interactions are handled

Short range method option menu: 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 text box: Specify the cutoff radius for the Cutoff method, in angstroms.
Tapering range text boxes: Specify the range in angstroms over which the force or the potential is tapered off in the two text boxes.

Scaled Effective Solvent scaling factor text box

Set a scaling factor for all nonbonded interactions. To use this feature for effective and efficient equilibration of polymeric systems, you could run MD steps starting with a scaling factor of 0.1 and increasing it in successive stages until the value is 1.0 (i.e. no scaling).

Using a reduced factor reduces the bias of the intrachain interactions, allowing chain structures to more closely resemble the actual chain conformations in a polymer melt or a water−polymer mixture, while still allowing rapid and efficient sampling of the polymer chain over all possible conformations and sampling the multiple basins in the potential energy surface. See Ref. 29 for more information.

This feature is only present for Molecular Dynamics stages in the MD Multistage Workflow Panel.

Restraints tab

In this tab you can specify restraints on atom positions. To define a restraint, you must specify the force constant for the restraint and provide an ASL expression for the atoms that are to be restrained.

Restraints table

Lists the restraints. You must enter the force constant for the restraint in the Force Constant column, in kcal/mol/Å². The Atoms column is filled in automatically when you click Select and use the Atom Selection dialog box to specify the atoms. Otherwise you can edit the cell to enter an ASL expression (see Atom Specification Language for details).

Select button

Opens the Atom Selection Dialog Box to specify the atoms for the selected restraint.

Only available if a single row is selected in the table. Not available for the MD Multistage Workflow Panel; you must edit the cell to enter an ASL expression.

Add button

Adds a restraint on a set of atoms. Clicking this button adds a row to the restraints table.

Delete button

Deletes the selected restraints.

Reset button

Resets the table to its default state.

Output tab

In this tab you can set names for various output files and directories, and set the times for which recording in these files begins and the update frequency. The default names include the variable $JOBNAME, which is set to the job name specified in the Job Settings Dialog Box. For replica exchange calculations the default names also include the variable $REPLICA, which indexes the replicas starting from 0. You should not remove the $REPLICA variable, as it is used to store results for each replica separately.

For each file or directory there is a starting time text box, in which you can enter the starting time for recording of information to this file or adjust the starting time in increments of 50 times the far time step (except for the checkpoint file, where the increment is 5000 times the far time step). Some files also have an interval text box, in which you can enter or adjust the recording interval (in the same increments as the starting time). The files or directories are listed below, with any extra controls. The periods for the energy sequence file and for the trajectory can be set in the Desmond panel and thus are omitted from the Output tab.

Energy sequence file text box

This file contains a sequence of various energies of the system.

Trajectory directory text box

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. There are two options for the trajectory:

Record velocities option: Record the velocities along with the coordinates. By default, they are not recorded, as it doubles the size of the trajectory.
Center trajectory on ASL text box and Define button: Center the trajectory on the atoms defined by the ASL expression in the text box. If the text box is empty, the trajectory is not centered. Enter the ASL expression in the text box, or click Define to open the Atom Selection Dialog Box to construct the ASL expression. For more information on ASL expressions, see Atom Specification Language.
Glue close solute molecules together option: Select this option to ensure that associated solutes appear together rather than on opposite sides of the simulation box. This option only affects the way the trajectory is displayed.

Checkpoint file text box

This file contains information that can be used to restart an interrupted simulation.

Misc tab

This tab provides access to various options that do not fit into the other categories. In this tab you can specify when and how the velocities are randomized, and specify atom groups for special treatment in the simulation.

Seed options

Select an option to specify the seed for random number generation.

Random—Use a seed selected at random. The seed changes each time it is used.
Custom—Use the seed specified in the text box. The same seed is used each time. This option allows you to reproduce the results of the velocity randomization.

Randomize velocities option and section

In this section you can randomize the velocities at a specific start time and interval, and specify a random number seed. By default velocities are randomized at the beginning of a calculation, and not randomized again. For some kinds of simulations (e.g. in the gas phase), periodic randomization of velocities can improve the sampling. When restarting from a checkpoint file, this option is off by default.

Starting time text box: Specify the time for the first randomization of the velocities.
Interval text box: Specify the interval at which velocities are randomized after the initial randomization.

Atom group section

In this section you can specify atom groups. Atom groups are used for various special treatments of atoms in the simulation. You can define multiple groups with the same name but a different index by setting the index in the Value column. Group 0 is the default group, to which all unassigned atoms automatically belong.

For example, if you define the thermostat atom group, each thermostat group index corresponds to a thermostat group in the Ensemble tab. Likewise, the energy group is used by the energy_group plugin, and the ligand group is used in absolute FEP jobs. Other groups can be defined for special treatment as needed.

Atom group table: Lists the atom groups. The Atoms column is filled in automatically when you click Select and use the Atom Selection dialog box to specify the atoms. Otherwise you can edit this column to specify the ASL expression for the atoms in the group. The number of atoms defined by the ASL expression is shown in the No. of Atoms column.
Select button: Opens the Atom Selection Dialog Box to specify the atoms for the selected group. Only available if a single row is selected in the table.
Add button: Adds an atom group. Clicking this button adds a row to the table.
Delete button: Deletes the selected groups. This operation can only be done on user-defined groups.
Reset button: Resets the table to its default state.

External electric field section

Set up an external electric field to be applied to the simulation box, in kcal/mol/e/Å or V/nm. Only available when this dialog box is opened from the MD Multistage Workflow Panel.

Note: The external electric field affects the velocities of the particles, producing a net velocity (positive or negative) along the direction of the field. The thermostat takes the velocities as they are (which includes the net velocity) in the evaluation of the temperature, so the calculated temperature is not the equilibrium temperature. This means that the thermal behavior of the system may not be what you expect.

Apply field text boxes: Specify the field to apply in each Cartesian direction by entering values in the text boxes.

Reset button

Discards changes made since the last set of changes were committed with the Apply button or the OK button, and resets the values to the last set committed.