[CP2K:1583] Re: Dcd file and VMD
teodor... at gmail.com
Mon Dec 1 14:57:34 CET 2008
no need to say anything else. I identified the problem. It is due to
some conflicts in different CVS commits.
I'm working now on a patch. Will send a message when the DCD will be
Thanks for reporting,
> 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.
> 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.
>> 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
>>> 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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