[gmx-developers] couple_moltype adds exclusions. why?

[Berk Hess]

On 11/25/12 21:46 , David van der Spoel wrote:
> Hi,
>
> I'm trying to desolvate a toluene molecule in order to compute the 
> free energy of solvation. Using mdp settings
>
> free_energy              = yes
> couple-moltype           = toluene
>
> all the non-bonded interactions within the molecule are excluded. Why? 
> The 1-4 interactions are not taken away, which should lead to 
> imbalance in the intramolecular interactions. Or am I missing something?
>
The intra-molecular non-bonded interactions are replaced by listed 
non-bonded interactions which always use the full interactions, without 
cut-off. This way the decoupled end state is a decoupled toluene in 
vacuum. This saves you from doing a vacuum calculation. It can also 
avoid sampling issues due to decoupling intra-molecular interactions. If 
you don't want this, an mdp option can turn this off.

Cheers,

Berk