[gmx-users] perturbation of charged groups

[K.A. Feenstra]

> 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?

A1: in principle there is no objection, but in practice, IIRC, free
energy perturbation is increasingly difficult for more charged systems.
I would guess what you are suggesting amounts to the worst possible case ;-(

A2: Don't know. That depends on what you want to calculate!

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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