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<DIV>Dear gromacs users,</DIV>
<DIV>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.</DIV>
<DIV>Q1: Does this variation of the charge influence the results of the free
energy calculation? (Is it wrong to simulate such a transformation?)</DIV>
<DIV>Q2: Is it better considering the neutral form of these groups, i.e. COOH,
NH2?</DIV>
<DIV>Thank you in advance for you suggestions.</DIV>
<DIV>Cristian</DIV></BODY></HTML>