G3X3 and VIRTUAL_SITES

[Pierre-André Cazade]

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

[Azade Yazdan Yar]

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

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[Pierre-André Cazade]

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 <pierre.a...@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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[Alin Marin Elena]

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/
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[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 

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[Matt W]

Constraints only work with MD not geo or cell opt.

[Pierre Cazade]

Hi Matt,

I have just realized going through the source code that shake is only used with MD.

Thanks,
Pierre

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