Dcd file and VMD

ilya ily... at gmail.com
Mon Dec 1 13:45:29 CET 2008


I've just updated my cp2k and found that when I'm trying to read dcd
in vmd now it prints an error

dcdplugin) read_dcdstep: corruption or unrecognized file structure

I decided that maybe it's due to changes discussed in this thread.
Could somebody explain how should i open new dcd.

Thanks,
Ilya.

On Nov 11, 2:43 am, Laino Teodoro <teodor... at gmail.com> wrote:
> I found a message from Axel with the necessary info (cell info format  
> in a dcd file) on another mailing list.
> I updated consequently the cell info in the dcd. Please try it and  
> let me know in case of further problems.
>
> Cheers
> Teo
>
> On 10 Nov 2008, at 23:53, Daniele Passerone wrote:
>
>
>
> > Dear Cp2k developers,
>
> > I use FIST on Cp2k version 2.0.0, with a system in a monoclinic cell
> > that I specify
> > by giving the three vectors A,B and C.
> > Indeed, in the output I get
>
> > INITIAL CELL ANGLS[deg]    =      0.9000000E+02   0.9000000E+02
> > 0.1199999E+03
>
> > The corresponding .dcd file contains in the array cell(6) only the
> > diagonal part of the cell (I read it with a Fortran program), so that
> > when it is read by vmd the periodic boundary conditions are wrong.
> > By the way, the
> >> molinfo 0 set alpha 120
> > command does not seem to have effect on my version of vmd (not
> > mentioning the fact that I should give this command for all frames).
> > It would be great to have the dcd file also with the cell lengths and
> > angle information...
>
> > Thank you in advance
> > Daniele Passerone


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