[gmx-users] perturbation of charged groups

[danciulescu at dwi.rwth-aachen.de]

Dear gromacs users,
I would like to calculate the free energy difference between two systems which involve the perturbation of charged groups (COO- to NH3+ or R(neutral) to COO- etc.). In this case the charge changes during the transformation from -1 to +1 etc.
Q1: Does this variation of the charge influence the results of the free energy calculation? (Is it wrong to simulate such a transformation?)
Q2: Is it better considering the neutral form of these groups, i.e. COOH, NH2?
Thank you in advance for you suggestions.
Cristian
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