VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 12 2010 - 15:28:06 CDT
- Next message: John Stone: "Re: Interaction Energy Using Python"
- Previous message: John Stone: "Re: Query regarding RMSD calculcation"
- In reply to: Parisa Akhski: "missing frames in trajectory file"
- Next in thread: Parisa Akhski: "RE: missing frames in trajectory file"
- Reply: Parisa Akhski: "RE: missing frames in trajectory file"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
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 Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns_at_ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
- Next message: John Stone: "Re: Interaction Energy Using Python"
- Previous message: John Stone: "Re: Query regarding RMSD calculcation"
- In reply to: Parisa Akhski: "missing frames in trajectory file"
- Next in thread: Parisa Akhski: "RE: missing frames in trajectory file"
- Reply: Parisa Akhski: "RE: missing frames in trajectory file"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]