Parameter setting for coordination number CV

[Junbo Lu]

Hello everyone,

  I need to simulate a liquid system where a metal ion is surrounded by water molecules. I hope to use coordination number as CV. I see the manual of PLUMED, but for some parameters, I can not make sure:

  How could we define d0 and r0? And how could we set the boundary of the coordination number?

  Could anyone give a help? I would be very appreciated!

  With my best regards,

  Junbo

[Giovanni Bussi]

Hi,

usually it is sufficient to set r0 to the first minimum of the radial distribution function.

You might want to check by plotting the switching function against the RDF that the switching function does not have a significant slope at distances BELOW the first maximum of the RDF. If it has a significant slope there, it might be better to increase d0 (and decrease r0 correspondingly, so that d0+r0 is still the first minimum). If the second maximum of the RDF is clearly defined, you might want to make sure that the slope goes to zero approximately at that distance.

Finally, you can significantly accelerate the calculation by using nighbor lists (set D_MAX and NLIST correctly). Have a look at point 2b here: https://www.plumed.org/doc-v2.7/user-doc/html/masterclass-21-7.html The solution will be actually posted on plumed_org youtube channel this evening.

Giovanni

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[Junbo Lu]

Hello Giovanni,

  Thank you for your comments!

  But I am confused. What do you mean plotting switching function against RDF? Do we use switching function value as y axis, and RDF value as x axis?

  With my best regards,

  Junbo 

Giovanni Bussi <giovann...@gmail.com> 于2021年5月3日周一 下午5:02写道：

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