VMD-L Mailing List

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Fri Jan 10 2014 - 10:06:47 CST

You can send me the code and I will take a look. What version of VMD are
you using and what is your OS?

On Thu, Jan 9, 2014 at 10:25 PM, Tristan Croll <tristan.croll_at_qut.edu.au>wrote:

> > This sounds more like a file not being properly closed to me.
>
> > Axel.
>
> I’m at a loss as to where that might be happening. I haven’t added any
> read/write entries to the code myself – all file handling is being done by
> calls to existing packages (mdff, ssrestraints, etc.). As far as I can
> tell they all seem to be fine at cleaning up after themselves.
>
>
>
> Tristan
>
>
>
> *From:* Axel Kohlmeyer [mailto:akohlmey_at_gmail.com]
> *Sent:* Friday, 10 January 2014 1:50 PM
> *To:* Tristan Croll
> *Cc:* Vmd l
> *Subject:* Re: vmd-l: strange problems adding extra bonds to interactive
> simulations
>
>
>
>
> On Jan 9, 2014 9:52 PM, "Tristan Croll" <tristan.croll_at_qut.edu.au> wrote:
> >
> > Hi,
> >
> >
> >
> > I’ve added the option to include secondary structure restraints to my
> gradually developing interactive MDFF extension (built from AutoIMD), and
> have run into a rather odd (and intermittent) problem.
> >
> >
> >
> > The call to ssrestraints in the code is fairly straightforward:
> >
> >
> >
> > # If secondary structure restraints are chosen, create restraints file
> >
> > if $settings::usessrestraints {
> >
> > package require ssrestraints
> >
> > ssrestraints -psf [file join "$settings::scratchdir" automdff.psf]
> -pdb [file join "$settings::scratchdir" automdff.pdb] -sel
> "$settings::ssrestraintsseltext" $settings::restrainhbonds -o [file join
> "$settings::scratchdir" automdff-ssrestraints.txt]
> >
> > mol delete top
> >
> > }
> >
> >
> >
> > ... as is the addition to the namd template file:
> >
> >
> >
> > # use secondary structure restraints if required
> >
> > if $usessrestraints {
> >
> > extraBonds yes
> >
> > extraBondsFile automdff-ssrestraints.txt
> >
> > }
> >
> >
> >
> > I’ve checked, and it creates a perfectly normal looking extrabonds
> file. However, when I run it, roughly 3 times out of 4 I get an “abnormal
> EOF” error with the diagnostic giving a line partway through
> automdff-ssrestraints.txt. The interesting thing is that it’s always
> truncating some power of two (2048, 4096 or 8192) characters into the file
> – which would suggest that a too-small chunk of memory is being
> pre-assigned for the file. But in that case, why does it vary from run to
> run (with identical conditions)?
> >
>
> This sounds more like a file not being properly closed to me.
>
> Axel.
>
> >
> >
> > I’m happy to send anyone a copy of the code to see if you can replicate
> the bug.
> >
> >
> >
> > Tristan Croll
> >
> > Lecturer
> >
> > Faculty of Health
> >
> > Institute of Health and Biomedical Engineering
> >
> > Queensland University of Technology
> >
> > 60 Musk Ave
> >
> > Kelvin Grove QLD 4059 Australia
> >
> > +61 7 3138 6443
> >
> >
> >
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> >
>