[CP2K-user] [CP2K:12641] Re: output trajectory not periodic by setting "PERIODIC XYZ-POISSON"

[Travis]

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 <javascript:>> 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
>>>>
>>>> -- 
>>>> You received this message because you are subscribed to the Google 
>>>> Groups "cp2k" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send 
>>>> an email to c... at googlegroups.com.
>>>> To view this discussion on the web visit 
>>>> https://groups.google.com/d/msgid/cp2k/99e88dd0-a25f-4b2c-8f2b-92afd080e603%40googlegroups.com
>>>> .
>>>>
>>> -- 
>> You received this message because you are subscribed to the Google Groups 
>> "cp2k" group.
>> To unsubscribe from this group and stop receiving emails from it, send an 
>> email to c... at googlegroups.com <javascript:>.
>> To view this discussion on the web visit 
>> https://groups.google.com/d/msgid/cp2k/74387394-44cc-483b-bb1b-c6120f36b1ec%40googlegroups.com 
>> <https://groups.google.com/d/msgid/cp2k/74387394-44cc-483b-bb1b-c6120f36b1ec%40googlegroups.com?utm_medium=email&utm_source=footer>
>> .
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20191215/0a61bb50/attachment.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: loadxyz.png
Type: image/png
Size: 66844 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20191215/0a61bb50/attachment.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: rightclick_loaddata.png
Type: image/png
Size: 87099 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20191215/0a61bb50/attachment-0001.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: top_molecule_selected.png
Type: image/png
Size: 106146 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20191215/0a61bb50/attachment-0002.png>