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

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

Dear Marcella,

I have studied the tutorial you provided. I used the method to my interest 
aqueous H2MoO4-H2O system. I want to monitor the structural change from 
octahedron (MoO2(OH)2(H2O)2) to octahedron (MoO3(H2O)3), i.e., a H atom in 
a hydroxyl of the former structure transfering to the other hydroxyl forms 
the latter structure.

I simulate so reaction by using a cube cell with 9.86 angstrom. ~32 waters 
were put into the cell. Two CVs was set: 1) the coordination number of the 
H atom to the hydroxyl O and 2) the coordination number of the H atom to 
the other hydroxyl O. 

However, the running results show when the H atom in a hydroxyl transfers 
to solvent, the octahedron (MoO3(OH)(H2O)2+) is unstable.  The 
 MoO3(OH)(H2O)2+ configuration transfers to tetrahedron MoO3(OH)-.

Therefore, a problem is if I can use some constraints to restraint the 
atoms which don't involve into the reaction.

Furthermore, how did you know the keywords in the cp2k software 
corresponding to the function or the expression? Would you have any 
specific manual? 

Thanks,

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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