CN as constraint for free energy calculation
Mengzi Zhou
smal... at gmail.com
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
&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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