NAMD is a widely used molecular dynamics simulation program. It lets users specify a molecule in some initial state and then observe its time evolution subject to forces. Essentially, it lets you go from a specific molecular structure to a simulation of its behavior in a particular environment. It has been used to study polio eradication, simulations of graphene, and studies of biofuels.

In this tutorial, we will learn how to run NAMD simulations on the OSG. We will perform the molecular dynamics simulation of Ubiquitin (pdb ID: 1UBQ) in implicit water.

NAMD tutorial files

It is easiest to start with the tutorial command. In the command prompt, type $ tutorial namd # Copies input and script files to the directory tutorial-namd.

This will create a directory tutorial-namd. Inside the directory, you will see the following files

namd_run.submit            # Condor job submission script file.
namd_run.sh                # Job execution script file.
ubq_gbis_eq.conf           # Input configuration for NAMD.
ubq.pdb                    # Input pdb file for NAMD.
ubq.psf                    # Input file for NAMD.
par_all27_prot_lipid.inp   # Parameter file for NAMD.

Here, namd_run.submit and namd_run.sh are the script files related to job submission and the other files are required by the NAMD software. The details regarding the preparation of input files for NAMD is available external website for NAMD at UIUC.

Job execution and submission files

The file namd_run.submit is the HTCondor job submission file. Here, we focus on the HTCondor file transfer mechanism relevant for this NAMD simulation example. The key word transfer_input_files specifies which input files are transferred from the login machine to the remote worker machine (where the jobs are being executed). In the namd_run.submit file, the option

transfer_input_files = ubq_gbis_eq.conf, ubq.pdb, ubq.psf, par_all27_prot_lipid.inp # list of input files needs to be transferred to the worker machine before.

means that the listed files are transferred from the login.osgconnect.net to the worker machine.

Similarly, we can transfer the output files from the worker machine to login.osgconnect.net by adding the following lines in the HTCondor job submission script file namd_run.submit:

transfer_output_files = file1.out, file2.out, file3.out ... # List of output files separated by commas.
should_transfer_files=Yes                                   # Key word to activate the file transfer
when_to_transfer_output = ON_EXIT                           # After the job execution is finished

However, in the vanilla universe transfer_output_files is not necessary as it transfers all the output files by default (the current example runs the job in the vanilla universe). The other script file namd_run.sh has the information about loading the namd module and the job execution commands:

module load namd/2.9                           
namd2 ubq_gbis_eq.conf > ubq_gbis_eq.$1.log # Here $1 is the argument from HTCondor job file

In essence, the NAMD simulation of a new molecule requires updating line 3 in namd_run.sh that executes the namd2 program and the list of file names for the keyword transfer_input_files in namd_run.submit.

Running the simulation

We submit the job using condor_submit command as follows

$ condor_submit namd_run.submit //Submit the condor job script "namd_run.submit"

Now you have submitted the NAMD simulation of ubiquitin in implicit solvent on the OSG. The present job should be finished quickly (less than an hour). You can check the status of the submitted job by using the condor_q command as follows

$ condor_q username  # The status of the job is printed on the screen. Here, username is your login name.

After the simulation is completed, you will see the output files (including restart and trajectory files) from NAMD in your work directory.

Getting Help

For assistance or questions, please email the OSG User Support team at user-support@opensciencegrid.org or visit the help desk and community forums.


This page was updated on Nov 12, 2019 at 00:00 from tutorials/tutorial-namd/README.md.