The instructions here assume you know the basics of running NAMD and have done it on a cluster like DT already. The details specific to Stampede2 are presented here. Stampede2 has 1T of space for each user, so clear out your data once in a while.

Your working directory should look similar to this\\
/work/04431/ewang125/stampede2\\
Note that you need the stampede2 directory.\\
Also, you can type ''cdw''  to go to your work directory. To setup your directory for group readability please do the following:

<code commend>
cdw
setfacl -d -m u:jklauda:rw .
</code>


Equilibrate your system on DT and get your restart files ''dyn.xsc'', ''dyn.coor'', ''dyn.vel''

In your namd directory, you need 5 more files to start production:\\
1. ''dyn.csh''\\
2. ''dyn.scr''\\
3. ''dyn-1.inp''\\
4. ''dyn-2.inp''\\
5. ''last.seqno''

Example files using the KNL nodes. Use 1 node per job!\\
{{ :prod.tar.gz |}}

Only dyn.csh changes if you're using the SKX nodes. For 30k atoms, 2 nodes is optimal. For 70k atoms, 3 nodes is ok but 4 is not ok. 4 tasks per node is recommended\\
{{ :dyn.csh.gz |}}

An important note: in ''dyn.scr'', you need to cd directly to the working directory. If you have a lot of jobs, you may find it tedious to change every file.