Thermophysical Properties Panel

Thermophysical Properties Panel Features

Use structures from option menu

Choose the structure source for the simulations. The structures must be Desmond model systems. Simulations for multiple structures are run concurrently.

• Project Table (n selected entries)—Use the entries that are currently selected in the Project Table or Entry List. The number of entries selected is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and select entries.
• Workspace (n included entries)—Use the entries that are currently included in the Workspace, treated as separate structures. The number of entries in the Workspace is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and include or exclude entries.
• File—Use the specified file. When this option is selected, the File name text box and Browse button are displayed. The allowed file types are: Desmond CMS.

Open Project Table button

Open the Project Table panel, so you can select or include the entries for the structure source.

File name text box and Browse button

Enter the Desmond CMS file name in this text box, or click Browse and navigate to the Desmond CMS file. The name of the Desmond CMS file you selected is displayed in the text box.

Compute density section

Specify the temperatures for which to calculate the density, and the settings to make for each choice.

Over a range of temperatures between T1 K and T2 K in steps of T K option and text boxes

Select this option to calculate the density over a range of temperatures. You can set the lowest and highest temperatures and the increment in temperature in the text boxes. The actual temperatures are generated by incrementing the lowest temperature. The highest temperature used is the one given in the text box (even if it is not in the series formed by incrementing the lowest temperature). This choice allows you to calculate the coefficient of thermal expansion and the glass transition temperature, using the Thermophysical Properties Analysis Panel.

Start each temperature with the converged system from the previous temperature option

Select this option to run the simulations sequentially, starting from the highest or the lowest temperature. The relaxation protocol is run on the model system at the first temperature in the sequence, followed by the simulation to converge the density at that temperature. The results are then used to start the simulation to converge the density at the next temperature, and so on. You can use a GPU to speed up the individual simulations.

Temperature protocol options

Specify the direction in which the sequential calculations are run:

• High to low—start at the highest temperature and decrease the temperature for each subsequent step, using the converged output from the previous step. Normal protocol for calculating T_g.

• Low to high—start at the lowest temperature and increase the temperature for each subsequent step, using the converged output from the previous step. Useful for examining melting behavior or other behavior on heating.

Run multiple temperatures simultaneously option

Select this option to run the simulation for each temperature at the same time. For each temperature, the relaxation protocol is run on the initial model system at that temperature prior to the simulation to converge the density. Select this option if you have multiple CPUs or GPUs available over which to distribute the simulations.

Change time step to n fs for temperatures above T K option and text boxes

Select this option to change the time step for simulations at temperatures above the specified temperature. Simulations at higher temperatures may require a shorter time step to obtain convergence.

Return converged structure closest to temperature text box

Specify the temperature for the simulation from which the output structure returned to Maestro is taken. The structure is the last frame from the converged simulation at the temperature closest to the one specified in the text box. Convergence is important: the output structure will not be taken from an unconverged simulation, so the nearest converged simulation is used to determine the output structure.

At a single temperature option and text box

Select this option to calculate the density at a single temperature, and specify the temperature in the text box. This choice gives you the density at the specified temperature, but no other properties.

Simulation time text box

Specify the desired simulation time in ps. This value is used for each simulation at each temperature. The time should be sufficient to converge the density, but may not exceed 200 ns.

Maximum cycles text box

Specify the maximum number of density simulations to perform to obtain a converged density. If the density does not converge in a simulation, another simulation is started from the output of the unconverged simulation, and this process is repeated until the density converges or the maximum number of density simulations specified here is reached. The total simulation time over all simulation cycles (product of the density simulation time and the maximum cycles) must not exceed 200ns.

Convergence text box

Density convergence criterion, as a percentage. The density convergence is calculated as the standard deviation of the density divided by the mean density, evaluated over the last 20% of the simulation cycle. If the percent density convergence is less than the value given, it is considered converged. The default is 5%.

Pressure text box

Specify the pressure to be used, in bar.

Barostat isotropy option menu

Choose the type of coupling for the barostat, from Isotropic or Anisotropic.

Relax model system before simulation option

When selected, a series of minimizations and short molecular dynamics simulations are performed to relax the initial model system before performing the simulation:

• 20 ps NVT Brownian minimization at 10 K,
• 20 ps NPT MD stage at 100 K,
• 100 ps NPT MD stage at temperature T

When the Start each temperature with the converged system from the previous temperature option is selected, T is the first temperature in the sequence. When the Run multiple temperatures simultaneously option is selected, T is every temperature step in the simulation to converge the density.

Normally, this option is needed only for model systems that have just been prepared (for example with the Disordered System Builder Panel) and have not been relaxed. This option is off by default.

Set random number seed option and text box

Select this option to specify a random seed to be used in the simulations. Specifying the seed allows you to reproduce the results, unless other factors affect them. If this option is not selected, a seed is chosen at random.

Save data section

Specify the data to save from the simulations.

Save intermediate data option and menu

Select this option to save data from the Desmond MD simulations. By default it is not selected, as the simulation files can be large and are not needed for the property analysis. The menu has two choices:

• CMS files—save the CMS files from each of the Desmond simulations. These are the files that contain the structure and force field information.
• CMS and trajectory—save the CMS files and the trajectories from each of the Desmond simulations. Note that trajectory files can be large and may take up a lot of disk space.

Combined trajectory option

Return a combined trajectory, which is generated by concatenating the trajectories from each run, in the order specified by the Temperature protocol option.

Energy file option

Return a energy file (.ene) which contains information on various energies at each time step of a simulation.

Trajectory recording interval text box

Set the recording interval for saving points on the trajectory, in ps. This is the amount of time between frames in the trajectory. The entered value is rounded to an integer multiple of the far time step size. The resultant number of records to be written is reported to the right.

Energy recording interval text box

Set the recording interval for saving energies, in ps. The resultant number of records to be written is reported to the right.

Cell parameters recording interval text box

Set the recording interval for saving the cell parameters, in Å. The resultant number of records to be written is reported to the right.

Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

The Job Settings button opens the Thermophysical Properties - Job Settings Dialog Box, where you can make settings for running the job.

Status bar

The status bar displays information about the current job settings and status for the panel. The settings includes the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.

Use the Reset button to reset the panel to its default settings and clear any data from the panel. You can also reset the panel from the Job toolbar.

The status bar also contains the Help button , which opens the help topic for the panel in your browser. If the panel is used by one or more tutorials, hovering over the Help button displays a button, which you can click to display a list of tutorials (or you can right-click the Help button instead). Choosing a tutorial opens the tutorial topic.

Related Topics

• Thermophysical Properties Analysis Panel
• System Builder Panel
• Disordered System Builder Panel
• thermophysical_properties_driver.py Command Help.
• Thermophysical Properties - Job Settings Dialog Box