How do I continue a Desmond simulation?

There are two scenarios for continuing a Desmond simulation: with the same parameters, or with modified parameters. These two scenarios use different files.

If you want to continue with the same parameters and number of processors, the easiest and most accurate way is to use the checkpoint file saved at the end of the simulation. To restart the simulation from Maestro, follow these steps:

1. Choose Applications → Desmond → task.
2. Choose Import from file in the Model system section.
3. Click Browse and navigate to the checkpoint file (.cpt).
4. Increase the total simulation time. (This is the only parameter that you can adjust.)
5. To avoid overwriting the files from the original simulation, do one of the following:
   • Change to a new working directory in Maestro, either by choosing Change Directory from the Maestro menu, or by using the cd command in the Commands text box.
   • Use a different job name when you start the job
6. Start the job.

To restart the simulation from the command line, follow these steps:

1. Open the .cfg file in a text editor.
2. Increase the value assigned to last_time. This is the total simulation time.
3. To avoid overwriting the files from the original simulation, either change to a new directory, or rename the .cfg, .cpt, and .cms files, before running the job
4. Start the job with the following command:
   
   $SCHRODINGER/desmond -exec mdsim -P processors -HOST host -restore checkpoint-file -c config-file
   
   The path to the checkpoint file and config file must be specified as the path from the new directory or to the renamed files. The value of processors must be the same as in the original job.

If you want to change the simulation parameters or run on a different number of processors you must use the output CMS file from the previous run. Since this file does not store all of the information to exactly continue the simulation, the new run will not be a strict continuation of the original simulation.

In particular, the velocities will be randomized again unless you increase the first randomization time to a value that is greater than the total (new) simulation time.

To restart the simulation from Maestro, follow these instructions:

1. Choose Applications → Desmond → task.
2. Choose Import from file in the Model system section.
3. Click Browse and navigate to the output CMS file (.cms).
4. If you want to start with the same settings as the previous job and make adjustments, click Read, and read the config file (.cfg)for the original job.
5. Increase the total simulation time, and make any other desired changes to the settings. In particular, adjust the Randomize velocities setting in the Misc tab of the Advanced Options panel to avoid velocity randomization.
6. To avoid overwriting the files from the original simulation, do one of the following:
   • Change to a new working directory in Maestro, either by choosing Change Directory from the Maestro menu, or by using the cd command in the Commands text box.
   • Use a different job name when you start the job
7. Start the job.

To restart the simulation from the command line, follow these steps:

1. Open the .cfg file in a text editor.
2. Increase the value assigned to last_time, and make any other desired changes to the settings. In particular, ensure that you include a randomize_velocity = {...} block with appropriate settings if you do not want the velocities randomized again.
3. To avoid overwriting the files from the original simulation, either change to a new directory, or rename the .cfg, .cpt, and .cms files, before running the job
4. Start the job with the following command:
   
   $SCHRODINGER/desmond -exec mdsim -P processors -HOST host -in cms-file -c config-file
   
   You will have to insert the path from the new directory to the CMS file and config file or use the new names.

Keywords: Desmond, continue simulation

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