VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 03 2014 - 16:36:47 CST

Hi guys,
  Most likely this is an issue with uninitialized data, a buffer overrun,
or something similar. Have you done tests with the failing input using
valgrind on Linux? If not, I'd try that first. If that works out fine,
then it's possible we're dealing with something that is indeed specific
to Windows, but most things that fail on Windows will also show up in
testing under Linux if one makes careful use of valgrind etc. I will
soon be making test builds of VMD 1.9.2 beta versions on Windows, so it
will be easier to track down anything that is truly unique to Windows
once I have those builds prepared.

Cheers,
  John

On Mon, Feb 03, 2014 at 07:09:13PM +0100, Olaf Lenz wrote:
> Hi!
>
> The trouble is that I do not have access to a Windows development system.
> With your message, I can have a look at the code again, but I am unable to
> compile or debug under Windows.
>
> Olaf
>
> Dr. rer. nat. Olaf Lenz
> Institut fA 1/4r Computerphysik, Allmandring 3, D-70569 Stuttgart
> Phone: +49.711.685.63607
>
> Am 03.02.2014 18:51 schrieb "Ming-Tsung Lee" <mtlee_at_rci.rutgers.edu>:
>
> Hi Olaf,
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/22262.html
> I think that I probably find the bug. In the VTF file generated by
> DL_MESO (attached, not sure the situation of ESPresSo). In the first
> frame of the trajectory, box dimensions are defined as follows
> timestep indexed
> pbc A 15.000000 15.000000 15.000000
> A A A A 0 10.867398 12.150888 14.039090
> A A A A 1 A 9.467130 10.474655 12.615115
> A A A A 2 A ...
> I have checked the default syntax of VTF. The box angles should be
> optional.
> https://github.com/olenz/vtfplugin/wiki/VTF-format
> I have played that around. It looks like that VMD is frozen while
> loading the line pbc/unitcell, as long as there are no "90 90 90"
> assigned. Nevertheless, the same VTF works perfectly well with the Linux
> version VMD. Would you please check your plugins for both platforms?
> Probably something is messed up in the Windows version. Thank you.
> For those who are using DL_MESO and want a quick solution for this,
> simply modify the trajectory output by putting a "90 90 90" after your
> box dimensions. It will work.
> Best,
> MT
> P.S. I am using Windows 7 x64 enterprise, VMD 1.9.1. Trajectory is
> generated from DL_MESO/DEMO/Polyelectrolyte/HISTORY, using
> /DL_MESO/DPD/utility/trajectselected.f90A
> Ming-Tsung Lee
> Department of Chemical & Biochemical Engineering
> Rutgers, The State University of New Jersey
> 98 Brett Road
> Piscataway, NJ 08854
> tel: 848-445-6953 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/