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

[Pierre-André Cazade]

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 <javascript:>> 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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