VMD-L Mailing List

From: Davit Hakobyan (davhak_at_gmail.com)
Date: Tue Mar 01 2016 - 04:37:49 CST

Thanks very much for your replies.

The over 5GB RAM memory is left free when this problems occurs in VMD so
most likely the problem relates to 4GB limit which Josh clarified. The
problem is that in this particular case I use VMD to convert the XTC file
to DCD format and I really need all the frames. So if there is no way to
convince VMD to read all 2000 frames (with stride 1) then I need to think
of some workaround like splitting the whole XTC to portions and feed them
separately to VMD and to have several sequential DCD files in the output.

Please let me know if a better solution exist.

Again, thanks a lot for any suggestion.

On Mon, Feb 29, 2016 at 10:35 PM, Josh Vermaas <vermaas2_at_illinois.edu>
wrote:

> Hi Davit,
>
> This sounds like you are on Windows and you have just passed the memory
> addressing limit vmd inherits by being a 32bit executable, which is 4gb.
> Once enough trajectory is loaded so that it passes the threshold, vmd can't
> address a memory location and crashes. Striding to reduce the loaded size
> is normally how people get around this, and use bigdcd ideas for analysis.
> If you go this route, I'd recommend converting the xtc to something else,
> since xtc frames aren't the same size on disk and so vmd can't read
> arbitrary frames efficiently, since it must read every intermediate frame.
> Josh
> On Feb 29, 2016 11:28 AM, Davit Hakobyan <davhak_at_gmail.com> wrote:
>
> Dear All,
>
> By now I was successfully loading XTC trajectory file containing 1500
> frames to VMD. Now as the simulation is still running and additional 500 ns
> were generated When trying to load the updated trajectory file containing
> 2000 frames VMD either crashes after loading some 1600 frames (if all the
> atoms are visible) or just stops randomly after loading 1623 ((the number
> can be different at different load attempts) frames (this is when only a
> selection like "resid 1" is active).
>
> Why I am basically sure that XTC file is correct is because when I try to
> load the same trajectory file with Stride 10, VMD then loads exactly 200
> frames.
>
> The XTC is generated on 64 bit Linux system and VMD is running on 64 bit
> Windows 7 with 12 GB of RAM, so memory is not a problem.
>
> The system size is ~74000 atoms.
>
> Does someone have any idea how to resolve this?
>
> Thanks a lot for any help.
>
>