fixing the bond distance between two atoms (non bonded)

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RUPESH TIWARI

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Apr 24, 2020, 10:46:45 PM4/24/20
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Dear all,
              I want to fix the distance between two atoms (non bonded) and optimise the whole systems using DFT in cp2k. Can anyone please tell me, how to fix the distance between two atoms. 

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Rupesh Kumar Tiwari 
C/o: Prof. Gopalan Rajaraman
Junior Research Fellow (CSIR)
Department of Chemistry
IIT Bombay
Mumbai- 400076

Sun Peng

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Apr 25, 2020, 12:26:59 AM4/25/20
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Hi, Rajaraman,
In my opinion, you can just fix the two atoms in three directions by adding the &CONSTRAINT subsection under the section MOTION. For more details, you can check the reference manual website: https://manual.cp2k.org/cp2k-7_1-branch/CP2K_INPUT/MOTION/CONSTRAINT.html

Penson 
Sun Yat-sen University

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祝您天天开心如意！
孙鹏 
中山大学 化学院
广东省广州市海珠区新港西路135号  510275
Your sincerely
Peng Sun

Patrick Gono

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Apr 25, 2020, 4:14:47 AM4/25/20
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Dear Rupesh,

You need to declare a collective variable representing the distance between the two atoms in the SUBSYS part of the FORCE_EVAL section. You specify the atoms by their indexes. Atoms are indexed in the order they appear in the coordinate section or the coordinate file. Indexing starts at 1:
    &SUBSYS
        ...
        &COLVAR
            &DISTANCE
                ATOMS  11  35
            &END DISTANCE
        &END COLVAR
    &END SUBSYS

Next, in the MOTION section, you set the collective variable to the desired value:
    &CONSTRAINT
        &COLLECTIVE
            TARGET   5.0833                   ! this value is in bohr
            INTERMOLECULAR T
            COLVAR 1                              ! index of the collective variable, in order of appearance in the SUBSYS section
        &END COLLECTIVE
    &END CONSTRAINT

I attach a sample input file for your convenience.

Yours sincerely,
Patrick Gono


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input.inp

Matt W

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Apr 25, 2020, 7:59:40 AM4/25/20
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This setting only works with MD, to my knowledge, not for GEO_OPT type runs. We don't (as far as I know) have any internal way of fixing particular bond lengths etc.
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祝您天天开心如意！
孙鹏 
中山大学 化学院
广东省广州市海珠区新港西路135号  510275
Your sincerely
Peng Sun

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Krack Matthias (PSI)

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Apr 25, 2020, 8:28:08 AM4/25/20
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Both atoms could be fixed to preserve their distance using https://manual.cp2k.org/cp2k-7_1-branch/CP2K_INPUT/MOTION/CONSTRAINT/FIXED_ATOMS.html

 

Matthias

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RUPESH TIWARI

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Apr 25, 2020, 8:32:09 AM4/25/20
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Thanks everybody for your valuable suggestions. 

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