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

[Jinyao Wang]

Hi gmx-users，

  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)

  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