VMD-L Mailing List

From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Thu Jan 09 2014 - 22:25:24 CST

> 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<mailto: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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>
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