[CP2K-user] [CP2K:12643] Re: output trajectory not periodic by setting "PERIODIC XYZ-POISSON"

[lizzy bai]

Dear Prof.Travis

Thank you very much for your help and patience.It works now.

Have a nice day
Best regards

Liyi

Travis <polla... at gmail.com> 于2019年12月15日周日 下午7:05写道：

> Hi,
>
> You've just loaded your coordinates incorrectly. Load XYZ first. Right
> click the line water-1.xyz, select Load Data Into Molecule. Ensure
> water-1.xyz is the molecule that is selected in the drop down menu. The
> default option in the Load Menu is to create a new molecule. Now just load
> the DCD. You will have a total number of frames equal to the number of
> frames in the DCD + 1 for the XYZ. You can print also to PDB which includes
> lattice, coordinate, and atom name data but sacrifices some precision as it
> writes fewer decimal places.
>
> -T
>
>
> On Sunday, December 15, 2019 at 2:20:00 AM UTC-5, lizzy bai wrote:
>>
>> Dear Prof.Travis
>>
>> Thank you very much for you reply.
>> Sorry, I have understood your points? "Convert the coordinates in your
>> input file to XYZ." Here what kind of input are you mentioning?
>>
>> I tried load the DCD and then load the xyz file. Then the the VMD
>> displayed like below.
>> Previously, I tried  load the lammps output  DCD file along with the psf
>> file, it woks well.
>> But for the cp2k output DCD, it doesn't work.
>> And, may I know it is possible to output both DCD and xyz files in CP2K?
>>
>>
>> Thank you very for your help
>>
>> best regards
>>
>> Liyi
>>
>> [image: WeChat Image_20191215160944.png]
>>
>> Travis <po... at gmail.com> 于2019年12月14日周六 下午5:19写道：
>>
>>> Hi,
>>>
>>> Convert the coordinates in your input file to XYZ. You need only a
>>> single snapshot. Then load the XYZ into VMD and select to load additional
>>> data into the molecule to append the DCD. The XYZ file is used just to add
>>> the atom names. You can also use one of the snapshots from your old XYZ
>>> trajectory to do this.
>>>
>>> -T
>>>
>>>
>>> On Saturday, December 14, 2019 at 3:04:56 AM UTC-5, lizzy bai wrote:
>>>>
>>>> Dear Prof. Travis
>>>>
>>>> Thank you very much for you information.
>>>> I have formated the trajectory as DCD. Then the outfile only has DCD
>>>> file, no xyz file. The following keywords I used as below:
>>>>  &TRAJECTORY
>>>>        FORMAT DCD
>>>>      &EACH
>>>>        MD 1
>>>>      &END EACH
>>>>    &END TRAJECTORY
>>>>
>>>> Best regards
>>>>
>>>> Liyi
>>>>
>>>> Travis <po... at gmail.com> 于2019年12月13日周五 下午10:45写道：
>>>>
>>>>> Hi,
>>>>>
>>>>> You load an XYZ first. Then load DCD as additional data. DCD doesn't
>>>>> contain atom names.
>>>>>
>>>>> -T
>>>>>
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