[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.
>
>-Justin
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
2009-10-12
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