How to understand the keywords atoms_from and atoms_to in the colvars??

Marcella Iannuzzi marci... at gmail.com
Wed Sep 9 17:24:27 CEST 2015


Dear Ning,

have a look at the following tutorial on MTD:
http://www.cp2k.org/exercises:2015_cecam_tutorial:mtd1
regards
Marcella


On Monday, September 7, 2015 at 1:02:24 PM UTC+2, ning.... at gmail.com 
wrote:
>
> I am newer for the cp2k. I am studying the metadynamics method. I noted 
> that colvars section in the input files includes the keywords atoms_from 
> and atoms_to. I don't understand what does it mean? what does the R_0 stand 
> for?? For example, see the bold text
>
> &FORCE_EVAL
>   METHOD Quickstep
>   &DFT
>     BASIS_SET_FILE_NAME BASIS_SET
>     POTENTIAL_FILE_NAME POTENTIAL
>     &MGRID
>       CUTOFF 200
>     &END MGRID
>     &QS
>     &END QS
>     &SCF
>       SCF_GUESS ATOMIC
>     &END SCF
>     &XC
>       &XC_FUNCTIONAL Pade
>       &END XC_FUNCTIONAL
>     &END XC
>   &END DFT
>   &SUBSYS
>     &CELL
>       ABC 5.0 5.0 5.0
>     &END CELL
>     &COORD
>     O   0.000000    0.000000   -0.065587
>     H   0.000000   -0.757136    0.520545
>     H   0.000000    0.757136    0.520545
>     &END COORD
>     &KIND H
>       BASIS_SET DZVP-GTH-PADE
>       POTENTIAL GTH-PADE-q1
>     &END KIND
>     &KIND O
>       BASIS_SET DZVP-GTH-PADE
>       POTENTIAL GTH-PADE-q6
>     &END KIND
>    * &COLVAR*
> *       &COORDINATION*
> *          ATOMS_FROM 1*
> *          ATOMS_TO 2 3*
> *          R_0 2.3*
> *       &END COORDINATION*
>     &END COLVAR
>   &END SUBSYS
> &END FORCE_EVAL
> &GLOBAL
>   PROJECT H2O-meta_coord
>   RUN_TYPE MD
>   PRINT_LEVEL LOW
> &END GLOBAL
> &MOTION
>   &MD
>     ENSEMBLE NVT
>     STEPS 10000
>     TIMESTEP 0.5
>     TEMPERATURE 300.0
>     &THERMOSTAT
>       &NOSE
>         LENGTH 3
>         YOSHIDA 3
>         TIMECON 100.0
>         MTS 2
>       &END NOSE
>     &END
>   &END MD
>   &FREE_ENERGY
>     &METADYN
>       DO_HILLS
>       NT_HILLS 2
>       WW 1.0e-3
>       &METAVAR
>         SCALE 0.02
>         COLVAR 1
>       &END METAVAR
>       &PRINT
>         &COLVAR
>            COMMON_ITERATION_LEVELS 3
>         &END
>         &HILLS
>            COMMON_ITERATION_LEVELS 3
>         &END
>       &END
>     &END METADYN
>   &END
> &END MOTION
>
> Any provides are welcome.
>
>
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