VMD-L Mailing List
From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Thu Jan 09 2014 - 22:25:24 CST
- Next message: Ricardo O. S. Soares: "Re: Display APBS on Solvent Accessible Surface"
- Previous message: Axel Kohlmeyer: "Re: strange problems adding extra bonds to interactive simulations"
- In reply to: Axel Kohlmeyer: "Re: strange problems adding extra bonds to interactive simulations"
- Next in thread: John Stone: "Re: strange problems adding extra bonds to interactive simulations"
- Reply: John Stone: "Re: strange problems adding extra bonds to interactive simulations"
- Reply: Ryan McGreevy: "Re: strange problems adding extra bonds to interactive simulations"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
> 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
>
>
>
> This email and its attachments (if any) contain confidential information intended for use by the addressee and may be privileged. We do not waive any confidentiality, privilege or copyright associated with the email or the attachments. If you are not the intended addressee, you must not use, transmit, disclose or copy the email or any attachments. If you receive this email by mistake, please notify the sender immediately and delete the original email.
>
>
>
>
- Next message: Ricardo O. S. Soares: "Re: Display APBS on Solvent Accessible Surface"
- Previous message: Axel Kohlmeyer: "Re: strange problems adding extra bonds to interactive simulations"
- In reply to: Axel Kohlmeyer: "Re: strange problems adding extra bonds to interactive simulations"
- Next in thread: John Stone: "Re: strange problems adding extra bonds to interactive simulations"
- Reply: John Stone: "Re: strange problems adding extra bonds to interactive simulations"
- Reply: Ryan McGreevy: "Re: strange problems adding extra bonds to interactive simulations"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]