restrain    = { atom = "asl:(chain.name A) AND (atom.ptype CA)" force_constant = 10.0 }

constraining protein CA or backbone is of great use when MD is producing based on homology models.

---------------Extract trajectory---------------
 
$SCHRODINGER/run -FROM desmond trajectory_extract_frame.py 6k_MD-out.cms --frames=4000 6k_MD_trj -o cms --asl='((chain.name A)) OR ((chain.name " "))'

Each frame of Desmond MD production can be extracted by above command line. New generated .cms file can be used as input file for new MD simulation.

--------------- Merge trajectory ---------------
 
$SCHRODINGER/run -FROM desmond manipulate_trj.py --mode merge out_trj $PATH/in_trj_1 $PATH/in_trj_2

Two or more trajectory can be merged by this command. This can be helpful for analyzing extended trajectory.

---------------Restart jobs---------------
 How do I continue a Desmond simulation?
A: 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. 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. (This is to avoid overwriting the files from the original simulation.) 
 
   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. Change to a new directory (to avoid overwriting the files from the original simulation.) 
 
   4. Start the job with the following command:
      $SCHRODINGER/desmond -exec mdsim -P processors -HOST host -restore checkpoint-file -c config-file

      You will have to insert the path to the checkpoint file and config file from the new directory. 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. 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. (This is to avoid overwriting the files from the original simulation.) 
 
   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. Change to a new directory (to avoid overwriting the files from the original simulation.) 
   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

 
---------------convert Amber system into Desmond format---------------
Using the Amber force field in desmond
The Desmond Users' Manual has instructions on converting Amber prmtop files to Maestro/Desmond format. As a small addition to that, here are some notes on how to convert the "jac" benchmark:

Run tleap -f leap.in, where this is the leap.in file:

    source leaprc.ff99SB
    x = loadpdb equil.pdb
    set x box 62.23
    saveamberparm x prmtop7 prmcrd7
    quit

2.  Run the following jobs to create a cms file:
    $SCHRODINGER/run amber_prm2cms.py -p prmtop7 -c prmcrd7 -o jac.cms
    [Note: the desmond manual says that you also have to run the
    "build_constraints.py" file, but Istvan Kolossvary reports that this
    is not necessary.]
the generated .cms is ready for Desmond simulation, you can skip the following step if you like.

3.  Open up a maestro window, use File -> Import Structures to open the
    jac.cms file.  Then go to Applications -> desmond; load the workspace
    structure into desmond; set up parameters you want, then select "write"
    to save the files under "jac_desmond".   You can then edit the
    jac_desmond.cfg file to remove unused blocks, and/or to tweak the input
    parameters.

    If you like, you can just edit the jac_desmond.cfg file in this directory,
    which is a cleaned-up version of one that Maestro created.
    [Note: it's not yet clear to me what is different between jac.cms and
    jac_desmond.cms, i.e. what if anything Maestro adds to the cms file.]
    If you add the following line at the end of the Desmond .cfg file,
    you'll get a detailed breakdown of timing and function calls.

    profile = {}

4.  To run the benchmark, type:

    $SCHRODINGER/desmond -HOST gyges -P 1 -c jac_desmond.cfg -in jac_desmond.cms

    where you substitute "gyges" for some entry in your schrodinger.hosts
    file in directory $SCHRODINGER.