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

[Mark Abraham]

Jinyao Wang wrote:
>> Jinyao Wang wrote:
>>> Hi gmx-users锛?
>>>
>>> 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. 
>>>
>> These terms should already be present in the .edr file.  Run g_energy and have a 
>> look.
>>
>> -Justin
> 
> 
> 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.

Since you only have solvent in your system, the entire non-bonded
contribution is from solvent-solvent interactions. That's already
reported in g_energy. If you're trying to ask about calculating
something else, please rephrase your question.

Mark