[gmx-users] How to exclude the interactions between molecule A and B in Gromacs?

Mark Abraham Mark.Abraham at anu.edu.au
Fri Aug 5 06:11:39 CEST 2011

On 5/08/2011 1:17 PM, DeChang Li wrote:
> Dear all,
> I want to use Gromacs to run an enhanced sampling molecular dynamics 
> (ESMD) proposed by Karplus's group (J. Am. Chem. Soc. (1990) 112, 
> 9161-9175. & J. Mol. Biol. (1999) 291, 101-115). In the ESMD 
> simulation, we need to exclude the interactions (especially the 
> Coulomb interactions) between some small molecules (e.g. ligand A and 
> its replica). How can Gromacs to do this? Any suggestion will be very 
> appreciated.

See energy groups and energy group exclusions in 3.3 and 7.3.19 of the 

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