From: Eric A Brenner (ericbrenner_at_utexas.edu)
Date: Mon Dec 12 2016 - 11:01:25 CST

Peter,

I tried running it in Bash, and instead of the Windows error, VMD just
closed itself with no warning or explanation. I did some testing and found
that if I run the loop on 10 files and then manually try to run it on an
11th in the same VMD session, I run into the problem. I ended up just
writing a Bash script to take 10 files at a time, run autopsf on them,
close VMD, reopen VMD, and repeat. Probably not the best solution, but it
seemed to work. It took a while, but I now have all of the PSF files I need
for NAMD.

-Eric

On Sun, Dec 11, 2016 at 2:32 PM, Peter Freddolino <petefred_at_umich.edu>
wrote:

> 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
> > >
> > >
> >
> >
> >
>
>