Here, you will submit and start a simulation. The details
of the simulation and how you will analyze it will be explained
in a later section. Since the
simulation will take some time to finish, you need to submit it
now so that when you reach analysis of the results,
your simulation will be completed.
The following files will be used for your NAMD job
cnt.psf
cnt.pdb
par_all27_prot_lipid.prm
initial.coor
initial.vel
sim_short.conf
1. Make sure you are in the nanotubes-tutorial working directory, using cd or dir in a terminal window.
2. Run the NAMD job. In the same terminal window, type:
| namd2 sim_short.conf |
Windows users: Instead of typing ``namd2", you will need to specify the full path to NAMD, depending on where you installed it. For example, if you installed namd2 in C:
NAMD, you would type: C:NAMDnamd2 sim_short.conf
You should now see NAMD's output indicating that the job is running.
Now let's move to the next section. You will come back to this job and analyze
the results after it has finished.