VMD-L Mailing List

From: Davit Hakobyan (davhak_at_gmail.com)
Date: Tue Mar 01 2016 - 14:11:45 CST

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--001a114101c6e39338052d025f20--