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

[ning.zh... at gmail.com]

Dear Marcella,

Thanks for your tutorial on MTD. 

Ning 

在 2015年9月9日星期三 UTC+8下午11:24:27，Marcella Iannuzzi写道：
>
>
> 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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