From: Peter Freddolino (petefred_at_umich.edu)
Date: Sun Dec 11 2016 - 14:32:00 CST

Hi Eric,
That’s pretty odd. We’ve successfully run autopsf in a loop like that on every structure in the pdb before, so it ought to work.
To figure this out further — can you send me a screenshot of the error message that comes up? Is anything else shown? Could you try waiting 5 minutes after it pops up the message to see if it is just being overzealous on declaring the program dead? I don’t ever use windows these days, but on mac os, I know that it sometimes unhelpfully flags vmd as nonresponsive when it is in the middle of some intense calculations. Also, does it die deterministically on the same file? If you make the problematic file first, does it get through 10 and then stop or does it die on the first one?

As an aside, what you’re doing would be syntatically cleaner if you instead did

set molid [mol new $file waitfor all]
autopsf -mol $molid -solvate -ionize
etc…

That way you’re not using the output from molinfo list (which should be a LIST) to set the molid for autopsf (which should be an integer). As written in this loop it doesn’t make a difference but it still hurts to look at, and is only even possible because tcl is so obnoxiously flexible about typing.
Best,
Peter

> On Dec 9, 2016, at 7:40 PM, Eric A Brenner <ericbrenner_at_utexas.edu> wrote:
>
>
>
> On Dec 9, 2016 6:35 PM, "Eric A Brenner" <ericbrenner_at_utexas.edu> wrote:
> Peter,
>
> So I've introduced the mol delete function and am now using these commands:
>
> set filelist [glob *.pdb]
> foreach file $filelist {
> mol new $file waitfor all
> set molid [molinfo list]
> autopsf -mol $molid -solvate -ionize
> mol delete all
> }
>
> However, when I run it, it gets through about 10 files (slowly), and then I get the message "winvmd has stopped working". I tried it on my desktop computer and had the same result.
>
> -Eric
>
> On Thu, Dec 8, 2016 at 9:00 PM, Peter Freddolino <petefred_at_umich.edu> 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…
> Best,
> Peter
>
> > On Dec 8, 2016, at 9:14 PM, Eric A Brenner <ericbrenner_at_utexas.edu> wrote:
> >
> > Peter,
> >
> > 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!
> >
> > Regards
> >
> > Eric
> >
> >
> >
> > On Dec 8, 2016 7:56 PM, "Peter Freddolino" <petefred_at_umich.edu> 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.
> >
> > Best,
> > Peter
> >
> > > On Dec 8, 2016, at 6:27 PM, Eric A Brenner <ericbrenner_at_utexas.edu> wrote:
> > >
> > > Hi,
> > >
> > > 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
> > >
> > > -Eric
> >
> >
>
>
>