From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Thu Jan 16 2014 - 13:22:47 CST

In your code, when the user selects the 'Submit' button, it looks like you
first call a routine which sets up the namd config file and all other
associated files, then go on to call namd itself. You are getting this
error because the setup code is not completing before you begin running
namd. It just so happens that the ssrestraints code is one of the last to
finish (it takes a few seconds to calculate the restraints), so when namd
starts up, it tries to read in an incomplete or nonexistent ssrestraints
file. I suggest perhaps having separate "Setup" and "Submit" buttons.

Also, I know you said this is a work in progress, but I caught a few other
bugs. For instance, the chirality restraint code doesn't seem to be called
even when selected, and if multiple restraints are selected, the resulting
configuration file is invalid because it sets the extraBonds parameter
multiple times. I'm the main MDFF developer, so if you would like help
with this plugin please feel free to email me directly and we could work on
this outside of VMD-l (if you want! This is something we have wanted to do
for a while but never got around to it).

On Sun, Jan 12, 2014 at 5:17 PM, Tristan Croll <tristan.croll_at_qut.edu.au>wrote:

> Hi Ryan,
>
>
>
> Hereís the tarball of the code. Despite the name change itís actually a
> rather straightforward extension on autoIMD Ė the change is simply because
> I wanted to keep the original autoIMD as well. I find it very useful,
> though. To answer your questions regarding versions, Iím currently using
> VMD 1.9.1. We had to build it from source against a newer VRPN library to
> make it work with the Novint Falcon, and after finally getting that working
> Iíve been loath to upgrade (apparently incorporating the latest VRPN
> version into the official package is on the to-do list in the near
> future). OS is Centos 6.4.
>
>
>
> Thanks,
>
>
>
> Tristan
>
>
>
> *From:* ryanmcgreevy_at_gmail.com [mailto:ryanmcgreevy_at_gmail.com] *On Behalf
> Of *Ryan McGreevy
> *Sent:* Saturday, 11 January 2014 2:07 AM
> *To:* Tristan Croll
> *Cc:* Axel Kohlmeyer; Vmd l
>
> *Subject:* Re: vmd-l: strange problems adding extra bonds to interactive
> simulations
>
>
>
> 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.
>
> Iím at a loss as to where that might be happening. I havenít added any
> read/write entries to the code myself Ė 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,
> >
> >
> >
> > Iíve 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
> >
> > }
> >
> >
> >
> > Iíve checked, and it creates a perfectly normal looking extrabonds
> file. However, when I run it, roughly 3 times out of 4 I get an ďabnormal
> EOFĒ error with the diagnostic giving a line partway through
> automdff-ssrestraints.txt. The interesting thing is that itís always
> truncating some power of two (2048, 4096 or 8192) characters into the file
> Ė 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.
>
> >
> >
> > Iím 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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