Desmond Tutorial

Desmond Tutorial
Running Desmond Simulations
Figure 6.1 Running a Desmond simulation
Select ‘Append new
entries’ to add results to
the current project.
Enter a name for the
simulation job.
Select the host where the
master job should run;
usually localhost.
Set job submission
parameters as needed.
Click the Start button.
2. Select Append new entries from the Incorporate field in the Output area to indicate that
results of the Desmond simulation should be added to the current Maestro project
(see “Maestro Projects” on page 24).
3. In the Master job area you can give the job a name and specify the username for job
submission. Normally, the master job should run on localhost, which is your workstation
where you launched Maestro. Use the options in the Subjob area to control
job submission parameters including the host on which the simulation subjobs will
run and the domain decomposition (the number of blocks into which the simulation
box will be split in the X, Y, and Z directions) that is compatible with the given number
of CPUs. On Figure 6.1 a cluster queue called swdev is shown, which allows a
maximum of 8 CPUs to be used by any one subjob and the domain‐decomposition is
set to 2x2x2. Note that for certain types of simulations, e.g., FEP simulations, multiple
subjobs can run simultaneously in which case the user may want to limit the
number of simultaneous subjobs submitted to a queue. This can be set in the Maximum
simultaneous subjobs field; zero means no limit and any nonzero value limits the
number of simultaneously submitted jobs to that value.
4. Click the Start button. The Desmond simulation process begins.
Running Simulations from the Command
Line
Given a valid .cms structure file and corresponding .cfg conguration file, the command
line syntax for running Desmond jobs is as follows.
$SCHRODINGER/desmond -HOST -exec -P
-c .cfg -in .cms
In case a job has to be restarted from a checkpoint file, replace the -c and -in options
with -restore and the name of the checkpoint file:
$SCHRODINGER/desmond -HOST -exec -P
-restore .cpt
66 D. E. Shaw Research September 2008