[CP2K:1583] Re: Dcd file and VMD

Teodoro Laino teodor... at gmail.com
Mon Dec 1 14:57:34 CET 2008


Ilya,
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 
again working.
Thanks for reporting,
Teo

ilya wrote:
> 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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