[CP2K-user] [CP2K:13528] G3X3 and VIRTUAL_SITES

[Matt W]

Constraints only work with MD not geo or cell opt.

On Wednesday, June 17, 2020 at 1:13:01 PM UTC+1, Pierre-André Cazade wrote:
>
> Hi Alin,
>
> Thanks for the example. I checked some of the regtest but not the one you 
> mentioned. This quite helpful. Yet, if you check my input file, this 
> exactly what I am doing, so I am puzzled as for why it seems the 
> constraints (at least g3x3) are not enforced. This leads to distorted water 
> molecules (I checked the restart file) and then to the bad contacts causing 
> cp2k to crash.
>
> Regards,
> Pierre 
>
> On Wednesday, June 17, 2020 at 1:02:19 PM UTC+1, Alin Marin Elena wrote:
>>
>> Hi Pierre, 
>>
>> there are some example in tests/Fist/regtest-1-3/h2o-32-g3x3-mult.inp 
>>
>>
>> Regards, 
>> Alin 
>>
>> Without Questions there are no Answers! 
>> ______________________________________________________________________ 
>> Dr. Alin Marin ELENA 
>> http://alin.elena.space/ 
>> ______________________________________________________________________ 
>>
>> On Wed, 17 Jun 2020 at 12:54, Pierre-André Cazade 
>> <pie... at gmail.com> wrote: 
>> > 
>> > Hi Azade, 
>> > 
>> > Thanks for your answer. The molname is defined in the PSF file, in the 
>> topology section. The molname seems to be identified correctly as it is 
>> present in the output file (attached) in the description of the topology. 
>> > 
>> > Regards, 
>> > Pierre 
>> > 
>> > On Wednesday, June 17, 2020 at 12:20:32 PM UTC+1, Azade Yazdan Yar 
>> wrote: 
>> >> 
>> >> Hi Pierre, 
>> >> I know some of the answers to your first question. 
>> >> What you use in the ATOMS should be the index of atoms within that 
>> molecule. Constraints will be applied to all molecules with the same 
>> MOLNAME or MOLECULE number. 
>> >> From your input file, I cannot see how the SWM4 molecules are defined 
>> in the coordinates section. You have to define the MOLNAME in that part as 
>> below (what I have as H2O, or MOLECULE 1). Note that if you use MOLECULE, 
>> it is the 'molecule kind number' and not molecule number. 
>> >> 
>> >> Hope this helps, 
>> >> Azade 
>> >> 
>> >> &G3X3 
>> >>        MOLECULE  1 
>> >>        ATOMS  1..3 
>> >>        DISTANCES     a b c 
>> >>  &END G3X3 
>> >> 
>> >> O    5.1692824047308950E+00    5.3185376653354242E+00   
>>  2.1483827179189252E+01 H2O 1 
>> >> 
>> >> On Wed, Jun 17, 2020 at 12:41 PM Pierre-André Cazade <
>> pie... at gmail.com> wrote: 
>> >>> 
>> >>> Dear CP2K users, 
>> >>> 
>> >>> I am trying to use G3X3 constraints on my water molecules during a 
>> CELL_OPT motion. Needless to say, that it does not work. The "manual" is 
>> not very clear about the indexes that need to be provided. Should I use the 
>> index of the atoms in the coordinate file, for example 15761 15762 15763, 
>> or the indexes within the water molecule itself: 1 2 3. Does such 
>> constraint apply to all my water molecules provided they have the same 
>> molname "SWM4" or do I need an entry for each water molecule? 
>> >>> 
>> >>> What about VIRTUAL_SITES? 
>> >>> 
>> >>> Finally, the "CONTRAINT_INFO ON" section does not print a single 
>> information in the output to help me out. 
>> >>> 
>> >>> I attached my input file for clarity. 
>> >>> 
>> >>> Regards, 
>> >>> Pierre 
>> >>> 
>> >>> 
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>>
>> > 
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>>
>>
>
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