CN as constraint for free energy calculation

Mengzi Zhou smal... at
Thu Jun 7 08:53:32 UTC 2018

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
                    TARGET 1.0
                    COLVAR 1
                             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 
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? 


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