VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 13 2015 - 14:52:23 CDT

Max,
  If you can provide me with an XTC file and an example VMD load command
that misbehaves when the stride parameter is used, that would be very helpful.
I just did some cleanup on the Gromacs plugins, so now is a good time to
exercise them a bit more.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Oct 01, 2015 at 04:56:13PM +0000, Ebert Maximilian wrote:
> Dear list,
>
> I am trying to open a XTC trajectory using a GRO structure file with a stride of 100. Every time I try that VMD 1.9.2 and 1.9.3a1 on Mac OS X 10.10.5 stops after a certain number of frames with the following message:
>
> 'Error reading timestep, file does not match format???
>
> I saw a previous discussion here on the list but the user stopped answering. I think I can give additional information. Without stride (i am converting the trajectory to strip the water molecules to fit the trajectory in the RAM) the XTC loads fine. Also the full trajectory passes gmx check, the RMSD looks as expected and does not jump at the frame in question, the energy, density, temperature, pressure, etc all look normal across the entire length. And finally converting the XTC file to a TRR file also works and loads the trajectory with stride in VMD (this time with all molecules including water). So maybe there is some problem between the way stride treats XTC? If you need any other inside or a more detailed bug report let me know.
>
> Regards,
> Max 

-- 
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/