[gmx-users] Re:Re: how to calculate the non-bond interaction between solvent and solvent in pure solvent system (Justin A. Lemkul)

Jinyao Wang wangjy at ciac.jl.cn
Mon Oct 12 04:33:05 CEST 2009

>> Hi Justin, Thank you for your reply. But I still don't know how to set the
>> "energygrps" option in the rerun.mdp for calculating the interaction between
>> solvent molecule and solvent molecule in pure solvent system. As you said
>> that these terms should be obtained running the g_energy,could you give me
>> some details about the "energygrps" option in rerun.mdp file or how to
>> calculate the intermolecular interaction in pure solvent system. Thanks in
>> advance. 
>If you have a pure solvent system, there is no way to set separate energygrps, 
>as you found out earlier.  There is also no need to re-run your simulation.  Use 
>g_energy to analyze your original ener.edr file; you will see the LJ and 
>Coulombic terms in the list of options.

Hi Justin,
 My simulation system is pure benzaldehyde system. I set the option nrexcl = 3. 
So I think the LJ and Coulombic terms include intermolecular interaction energy and intremolecular interaction eneryg (e.g. between atom and atom)



        Jinyao Wang
        wangjy at ciac.jl.cn

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