VMD-L Mailing List

From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Thu Jan 16 2014 - 14:57:31 CST

That's definitely not an explanation I would have caught. Thanks very much for taking the time!

From: ryanmcgreevy_at_gmail.com [mailto:ryanmcgreevy_at_gmail.com] On Behalf Of Ryan McGreevy
Sent: Friday, 17 January 2014 5:23 AM
To: Tristan Croll
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: strange problems adding extra bonds to interactive simulations

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<mailto:tristan.croll_at_qut.edu.au>> wrote:
Hi Ryan,

Here's the tarball of the code. Despite the name change it's actually a rather straightforward extension on autoIMD - 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, I'm 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 I've 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> [mailto: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<mailto: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<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
>
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