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You need to ensure that the relevant NAMD files are in the directory were you wish to submit your job from. Run qnamd_2.11 in order to generate a PBS script and submit a job to the cluster. Examples of the script are provided below:

Examples of input required for these scripts are provided below.

                  EXAMPLE1
Enter project name/shortname
CHEM0100
Enter input file (with .conf extension)
test.conf
Enter number of nodes on which to run job
1
Enter total walltime (hour:minute)
2:00
Enter email address
testing@gmail.com
Generated pbs file for test
Do you wish to submit job to cluster (y/n)
y

  EXAMPLE2 [PLEASE TAKE NOTE OF EMPTY SPACES]
Enter project name/shortname
CHEM0100
Enter input file (with .conf extension)
test.conf
Enter number of nodes on which to run job

Enter total walltime (hour:minute)

Enter email address
testing@gmail.com
Generated pbs file for test
Do you wish to submit job to cluster (y/n)
y