[gmx-users] how to calculate the non-bond interaction between solvent and solvent in pure solvent system

[XAvier Periole]

> I want to calculate the non-bond interaction (LJ+Coulomb) between  
> solvent and solvent in pure solvent system.
>  After the simulation of my pure solvent system, I calculated the  
> interaction between solvent and solvent using the rerun option of  
> the "mdrun program".
>  First, I set the  energygrps = sol sol  in rerun.mdp file.
>  Then, I make the grompp program like this,
>  grompp -f rerun.mdp -c conf.gro -n index.ndx -p pure.top -o rerun.tpr
>  But this step has a fatal error: Atom 1 in multiple energy Mon.  
> groups (1 and 2)
This option can only calculate energies between non-overlapping groups.
That what he message is telling you: one atom can not be part of
more than one group.

If you actually have a simulation of pure solvent the total non-bonded  
energy
of your system seems to be what you are looking for!
>
>  I don't know how to solve the problem and I want to know whether  
> this method is effective for calculating the interaction between  
> solvent and solvent in pure solvent system.
>
> Any suggestion will be appreciated.
> 	
>
>
> 				
>
> 　　　　　　　　Jinyao Wang
> 　　　　　　　　wangjy at ciac.jl.cn
> 　　　　　　　　　　2009-10-10
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