[CP2K-user] how to constraint the H2O molecule using the G3X3

ning zhang ning.z... at gmail.com
Thu May 9 02:01:14 UTC 2019

Thanks for your advice. I have running the MD of FIST method with psf file. 
Thanks again.


在 2019年5月9日星期四 UTC+8上午12:35:28,Travis写道:
> As I mentioned previously, CP2K stumbles over your close contact. You 
> would have to manually edit the generated PSF file to correct the issues. 
> Alternatively, you can open your structure in a molecular editor and just 
> drag the offending water away from the other water OR recreate your 
> structure in Packmol with a cell that's about 1.2 - 1.5x the size you 
> expect, then let it relax during MD with your force field. This is a very 
> common strategy to cope with Packmol's tendency to generate close contacts 
> between peripheral atoms, even with the distance constraints.
> -T
> On Tuesday, May 7, 2019 at 4:10:05 AM UTC-3, ni... at gmail.com wrote:
>> Hi Travis,
>> Thanks for your reply. Indeed, I have attempted to generate the 
>> connectivity file (***.psf) by the CP2K.  I can successfully run the test 
>> input file (see the h2o-32-g3x3-mult.inp in tests). However, it seems to 
>> have some bugs (see attachment) in the CP2K when I modified the 
>> coordination values according to my case (other parameters is same as those 
>> in h2o-32-g3x3-mult.inp). Would you have any experiences about this?
>> 在 2019年5月7日星期二 UTC+8上午1:04:59,Travis写道:
>>> Append 'H2O' as the 5th column in the XYZ coordinates for waters. You 
>>> can provide a connectivity file or allow CP2K to generate one, see 
>>> https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/TOPOLOGY.html#list_CONN_FILE_FORMAT. 
>>> You can then modify this file to define 'H2O'. The automatic generation 
>>> will probably mess up on your close contact, so be sure to double check 
>>> that. The bit below will function to hold the bonds constant but it needs 
>>> to know what 'H2O' is in your model. Change the distances to reflect the 
>>> water model you're using.
>>> <within CONSTRAINTS>
>>>     &G3X3
>>>       DISTANCES [angstrom] 1.0 [angstrom] 1.0 [angstrom] 1.63298
>>>       MOLNAME H2O
>>>       ATOMS 1 2 3
>>>     &END G3X3
>>> On Monday, May 6, 2019 at 12:58:22 PM UTC-3, ni... at gmail.com wrote:
>>>> Hi everyone,
>>>> I am running the MD using the FIST method for a cell including one CaF 
>>>> and 61 H2O. To avoid the decomposition of water molecule, I want to 
>>>> constraint the O-H bond of 61 water molecules using G3X3. However, it seems 
>>>> that there has some bugs in the input file. I have attached the input file. 
>>>> Would you please to have a look? Any points are welcome.
>>>> Best,
>>>> Ning
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