[CP2K-user] [CP2K:20243] Re: Why the CV values (Coordination Number) is negtive in the metadynamics calculation

[贾建峰]

Hi Marcella,




So, another question, what is the meaning of the first column data in the fes.dat? Is it not the CV values?  




Regards

Jianfeng Jia 







At 2024-05-26 21:51:45, "Marcella Iannuzzi" <marci.akira at gmail.com> wrote:

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       -0.0015031205
       -0.4790510169       -0.0023662732
       -0.4453739259       -0.0036245468
       -0.4116968348       -0.0054030940
       -0.3780197438       -0.0078403220
       -0.3443426527       -0.0110778295
       -0.3106655617       -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








-- 
You received this message because you are subscribed to the Google Groups "cp2k" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/2d383898.7ff0.18fb90eb6e3.Coremail.jjf_sxnu%40163.com.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20240527/6c354036/attachment.htm>