[CP2K-user] [CP2K:13169] fixing the bond distance between two atoms (non bonded)

[RUPESH TIWARI]

Thanks everybody for your valuable suggestions.

On Sat, 25 Apr 2020, 5:58 pm Krack Matthias (PSI), <matthi... at psi.ch>
wrote:

> 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
>
>
>
> *Von:* cp... at googlegroups.com <cp... at googlegroups.com> *Im Auftrag von *Matt
> W
> *Gesendet:* Samstag, 25. April 2020 14:00
> *An:* cp2k <cp... at googlegroups.com>
> *Betreff:* Re: [CP2K:13169] fixing the bond distance between two atoms
> (non bonded)
>
>
>
> 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.
>
>
> On Saturday, April 25, 2020 at 9:14:47 AM UTC+1, Patrick Gono wrote:
>
> 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
>
>
>
>
>
> On Sat, 25 Apr 2020 at 06:26, Sun Peng <sp... at gmail.com> wrote:
>
> 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
>
>
>
> On Sat, 25 Apr 2020 at 10:46, RUPESH TIWARI <rup... at gmail.com> wrote:
>
> 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.
>
>
>
> --
>
> Rupesh Kumar Tiwari
>
> C/o: Prof. Gopalan Rajaraman
>
> Junior Research Fellow (CSIR)
>
> Department of Chemistry
>
> IIT Bombay
>
> Mumbai- 400076
>
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> --
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> *祝您天天开心如意！*
>
> *孙鹏*
>
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> *Peng Sun*
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