CN as constraint for free energy calculation

[Mengzi Zhou]

Thanks so much, Marcella.
In this case, I think the average and the sum would do the same effect.

在 2018年6月7日星期四 UTC+8下午4:58:52，Marcella Iannuzzi写道：
>
> Dear Mengzi, 
>
> The variable as you defined it takes the average of the coordination of 
> the ATOMS_FROM.
> 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
> Marcella
>
>
> 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
>> &COORDINATION
>>           ATOMS_FROM 7 25
>>           ATOMS_TO 15 16 17 18
>>           ND 18
>>           NN 10
>>           R0 [angstrom] 2.7
>> &END COORDINATION
>> …………
>> &CONSTRAINT
>>          &COLLECTIVE
>>                     TARGET 1.0
>>                     INTERMOLECULAR
>>                     COLVAR 1
>>          &END COLLECTIVE
>>          &LAGRANGE_MUTIPLIERS
>>                      FILENAME=force1.0
>>                      &EACH
>>                              MD 1
>>                      &END EACG
>>          &END LAGRANGE_MUTIPLIERS
>> &END CONSTRAINT
>>
>> 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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