VMD-L Mailing List

From: Eric A Brenner (ericbrenner_at_utexas.edu)
Date: Fri Dec 09 2016 - 18:40:15 CST

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
> >
> >
>
>