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

[Krack Matthias (PSI)]

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<javascript:>> 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<javascript:>> 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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