CN as constraint for free energy calculation

Marcella Iannuzzi marci... at
Thu Jun 7 08:58:52 UTC 2018

Dear Mengzi, 

The variable as you defined it takes the average of the coordination of the 
If you want to use the sum of the coordinations of each of the specified 
atoms in ATOMS_FROM, you need to define a COMBINED collective variable, 
where you set the sum of coordinations of single atoms.
Kind regards

On Thursday, June 7, 2018 at 10:53:32 AM UTC+2, Mengzi Zhou wrote:
> Dear all,
>           Recently I use CN as the constraint for free energy calculation 
> for Mg2+ ---  sulfate anion ----Mg2+ in water. CN is defined as the 
> coordination number of two Mg atoms to four O atoms in SO4(2-). The 
> below is related part in input file
>           ATOMS_FROM 7 25
>           ATOMS_TO 15 16 17 18
>           ND 18
>           NN 10
>           R0 [angstrom] 2.7
> …………
>          &COLLECTIVE
>                     TARGET 1.0
>                     INTERMOLECULAR
>                     COLVAR 1
>          &END COLLECTIVE
>                      FILENAME=force1.0
>                      &EACH
>                              MD 1
>                      &END EACG
> At first, I set TARGET 1.9, because I thought this constraint is for the 
> sum of both Mg, and by a free AIMD run two Mg are both collected to SO4. 
> But I checked the result of TARGET 1.9 and found SO4 structure got 
> distorted largely. It seems that each Mg is under the constraint of 1.9 not 
> the sum of 2 Mg. So I retry with TARGET 1.0. This time, the trajectory is 
> realistic. Both Mg are collected to SO4 just like what happens in free AIMD 
> run. 
> I want to ask when several atoms are in ATOMS_FORM or KINDS_FROM section, 
> whether the TARGET constant is for each one of them or the sum of them? 
> From my tests, it seems the former one. If so, what should I do to make the 
> sum of them be the constraint? or it cannot be done by methodology due to 
> more than one degree of freedom? 
> Sincerely,
> Mengzi.
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