[gmx-users] Trifluoroethanol-Ethanol mixtures study

[Mark Abraham]

On 4/01/2011 9:55 PM, Marcelo Silva wrote:
> Thank you Mark,
>
> But in the case of trifluoroethanol:
>
> C(F)   0.5323        1
> F       -0.2057        1
> F       -0.2057        1
> F       -0.2057        1
> C(H)   0.1263        2
> H(C)   0.0825        2
> H(C)   0.0825        2
> O       -0.6351        2
> H        0.4286        2
>
> The total charge is zero, but if we take the same pattern as for 
> ethanol, the charge group 1, for example, don't add to zero.

OK, so what did the author of these charges have to say about that, and 
in what manner did they intend to use it? Did their observations justify 
their parameters?

> In the manual it says "When all chemical moieties have a net charge 
> ofzero, these jumps can be reduced by moving groups of atoms with net 
> charge zero, called charge groups, in and out of the neighbor list", 
> that's why I have this question.

There's am unspoken caveat there that this is important when using an 
electrostatics method that only treats the atoms that are in the 
neighbour list. With PME, this question becomes moot.

Mark