From: Vermaas, Joshua (
Date: Fri Dec 09 2016 - 13:30:38 CST

As an extra little piece of advice, I’d test this on your laptop first, and put a “puts” statement somewhere in your loop so you can see progress (maybe outputting the pdb code for the file its working on), since what you describe is what I tend to see when VMD is working hard on something if I give it a huge list to churn through. If I’m building a new script, I tend to build it up by testing a single loop iteration first (by putting an “exit” at the end of the loop), and then invariably fixing the oversights I made as I go from 1 to many iterations. On supercomputers where you tend to work by script, you can pass the script as a command line argument (see to execute it:

vmd -dispdev text -e scriptname.tcl

The admins I’ve worked with so far haven’t complained about using the login nodes for these sorts of runs, mostly since if its written well it won’t take too long to execute.

Josh Vermaas

Director’s Postdoctoral Fellow
National Renewable Energy Laboratory<>

On Dec 8, 2016, at 8:00 PM, Peter Freddolino <<>> wrote:

In that case, the apparent freeze that you experienced may just have been vmd being nonresponsive while it was working on all of the structures. You might want to check if output is being generated before killing it…

On Dec 8, 2016, at 9:14 PM, Eric A Brenner <<>> wrote:


Thanks for the reply. I should have been more clear about the program 'crashing'. I meant that VMD freezes, and I have to force close it. I wasn't using mol delete, so I'll make sure to change that!



On Dec 8, 2016 7:56 PM, "Peter Freddolino" <<>> wrote:
Dear Eric,
You should in fact be able to run autopsf on plenty of files on your laptop. You don’t give any details with ‘the program crashed’ to help troubleshoot, but my guess is that you ran the machine out of memory by not deleting the molecules after you were done with them (by using mol delete), and thus they accumulated in memory. The situation won’t be much better on the login node of a supercomputer, which isn’t all that much more powerful in most cases than a decent workstation.

The vmd prompt that you got will accept commands like the tkcon. Try running
module load autopsf

and then things should work. But I do not recommend doing this on a supercomputer login node — they’re not designed for heavy lifting, and you’re likely to hack off the local admins.


On Dec 8, 2016, at 6:27 PM, Eric A Brenner <<>> wrote:


I have about 900 pbd files of small peptides that I plan on running in NAMD. I'm currently at the step of generating PSF files. I wrote a loop in Tk Console to test it on a handful of them, and it worked fine. When running it on all of the pdb files using my laptop, the program crashed. I have access to a supercomputer which I assume I'll have to use. The interface with the supercomputer is Bash. I ran VMD and got to this interface:

Info) Dynamically loaded 2 plugins in directory:
Info) ~/vmd-1.9.3/lib/vmd/plugins/LINUXAMD64/molfile
vmd >

Can I treat this as the Tk Console? If not, how can I run autopsf on it?
I tried running autopsf on one of my files and it said:

invalid command name "autopsf"

I've done a lot of Googling and looked through the tutorials, but I'm still unsure what to do. I'm relatively new to computational work, so forgive my ignorance.

Thank you