From: Davit Hakobyan (davhak_at_gmail.com)
Date: Tue Mar 01 2016 - 23:39:41 CST

Hi,

For those who might be interested the xtc trajectory can be read with
catdcd by adding "-xtc" flag, so the complete command should look like:

catdcd.exe -o out.dcd -first 1 -stride 1 -stype gro -s in.gro -xtc in.xtc

catDCD indeed did the job.

Thanks a lot for all suggestions and special thanks to Ajasja! ;)

On Tue, Mar 1, 2016 at 9:11 PM, Davit Hakobyan <davhak_at_gmail.com> wrote:

> Thanks a lot for all suggestions.
>
> I am trying to use catDCD with the following arguments:
>
> catdcd.exe -o out.dcd -first 1 -stride 1 -stype gro -s in.gro in.xtc
>
> but it gives the following error:
>
> dcdplugin) unrecognized DCD header:
> dcdplugin) [0]: 1995 [1]: -1105264384
> dcdplugin) [0]: 0x000007cb [1]: 0xbe1f0100
> dcdplugin) read_dcdheader: corruption or unrecognized file structure
> Error: could not open file 'in.xtc' for reading.
>
> It apparently tries to open the xtc file as having a dcd format. Is there
> a way to mention not only the initial structure file type (stype) but also
> the trajectory file type? Or how to workaround this?
>
> Thanks again for any help
>
>
> On Tue, Mar 1, 2016 at 12:02 PM, Ajasja Ljubetič <
> ajasja.ljubetic_at_gmail.com> wrote:
>
>> Hi Davit!
>>
>> For the conversion you could try the 64 bit catDCD that Axel
>> cross-compiled a while ago for.
>> http://rpm.lammps.org/windows/testing/
>>
>> Best,
>> Ajasja
>>
>>
>>
>> On 1 March 2016 at 11:37, Davit Hakobyan <davhak_at_gmail.com> wrote:
>>
>>> 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.
>>>>
>>>>
>>>
>>
>