VMD-L Mailing List

From: Parisa Akhski (Parisa.Akhshi_at_chem.queensu.ca)
Date: Tue Oct 12 2010 - 16:33:12 CDT

Hi John,
I think I figured out what the problem is. You may look at the discussion on NAMD mailing list for this problem:

http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/12866.html

Thanks for your reply,
Parisa

-----Original Message-----
From: John Stone [mailto:johns_at_ks.uiuc.edu]
Sent: Tue 10/12/2010 4:28 PM
To: Parisa Akhski
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: missing frames in trajectory file
 

Hi,
  How big is your DCD file, and what operating system and version of
VMD are you trying to load the DCD file with? Did you copy the DCD file
over a network at some point (e.g. could it have been truncated), or are
you reading it directly from the machine where the simulation was done?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Oct 06, 2010 at 06:49:29PM -0400, Parisa Akhski wrote:
> Dear VMD users,
>
> I have just finished the MD simulation of a DNA system. I had to restart
> the job three times. Now, I am looking at the trajectory of the system.
> The problem is that the number of the frames at two of the restarted jobs
> is not what it is supposed to be. In fact, many of the frames are missing.
> I can see that in the output file, it says:
>
> WRITING COORDINATES TO DCD FILE AT STEP ....
>
> for all the frames expected. But, I don't know why it doesn't show up in
> the dcd files that I am loading in VMD. Does anyone have any idea please?
>
> Thanks,
> Parisa 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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