[CP2K-user] [CP2K:20240] Re: Why the CV values (Coordination Number) is negtive in the metadynamics calculation

[Marcella Iannuzzi]

Hi Jianfeng Jia

The CV is never negative, as reported in the COLVAR output. 
In the first part of the simulation, it is almost zero, and the 
metadynamics hills have a width of 0.2, meaning that they extend to 
negative values.

Regards
Marcella

On Sunday, May 26, 2024 at 9:38:31 AM UTC+2 jjf_sxtu at yahoo.com.cn wrote:

> Dear CP2K experts,
>  I want ot use cp2k to do a metadynamics calculation to get the free 
> energy change for a reaction. I use the coordination number of a  O atom to 
> all H atoms as CV (this O-H bond will be formed in the reaction) to do the 
> metadynamic calculation.  
> the CV was defined as:
>          &COLVAR
>           &COORDINATION
>              ATOMS_FROM  61
>              KINDS_TO H
>              R0 [angstrom] 0.93
>              NN 8
>              ND 14
>           &END COORDINATION
>           &END COLVAR
>
> For metadynamics:
>
>     &METADYN
>       DO_HILLS
>       NT_HILLS 80
>       WW 3.0e-3
>
>       &METAVAR
>         SCALE 0.2
>         COLVAR 1
>       &END METAVAR
>
> When the job was ended, I get the fes.dat file by using the command: 
> graph.psmp -cp2k -ndim 1 -ndw 1 -file aimd-1.restart. This file looks like:
>        -0.5800822901       -0.0005584043
>        -0.5464051991       -0.0009289081
>        -0.5127281080 <(512)%20728-1080>       -0.0015031205
>        -0.4790510169       -0.0023662732
>        -0.4453739259 <(445)%20373-9259>       -0.0036245468
>        -0.4116968348       -0.0054030940
>        -0.3780197438       -0.0078403220
>        -0.3443426527       -0.0110778295
>        -0.3106655617 <(310)%20665-5617>       -0.0152462075
> ........
>
> My question is why the CV vaules in the first column can be negative?  My 
> CV is the coordination number. I think it should be positive anyway.  The 
> whole input file and corresponding xyz file and some output file were 
> attached in this letter. Please help me.
>
> Jianfeng Jia
>
>
>
>

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