How did I set the H atom as a “dummy” atom?

ning.zh... at ning.zh... at
Fri Jun 12 10:52:34 UTC 2015

Hi all,

I am using thermodynamic integration to compute free energy change and, 
finally, I will obtain the pka (acid constant). To 

get the MD trajectory of intermediate states between initial and final 
states, I am using mixed type calculation of the 

two end states. In the two force_eval sections corresponding to two end 
states, I have to impose different restraints of some colvars. Let us use 
the reaction H3O+ ---> H2O + H as an example. To describe the deproton of 
the H3O+, it needs to obtain the free energy of this reaction. Considering 
to the computation cost, one often use the 5-point simpson rule to 
calculate the deltA. Furthermore, the charge of H atom is swithch off as a 
"dummy" atom. And then, the averages of vertical energy gaps are calculated 
over the restrained mapping Hamiltonian: H = (1-k)HR + kHP + Vr(HR is the 
hamiltonian of reactant and HP is the hamiltonian of product, Vr is 
restrained harmonic potential). However, Some confusions are available:
1) How did I set the H atom as a dummy atom?
2) I have written a input file. Does anybody have experience about this?

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