[gmx-users] Ionic liquid simulation problem

Ednilsom Orestes eorestes at gmail.com
Wed Sep 6 16:51:44 CEST 2017

Hi Ghosh,

Thanks for your answer.
But I'm not sure if I understood what you meant.
I already used insert-molecules command to create a box with the cationic
Now, should I use the same command to include the anionic species into the


*Prof. Dr. Ednilsom OrestesDepartamento de Ciências Exatas - Sala C19Escola
de Engenharia Industrial Metalúrgica de Volta Redonda*

*Universidade Federal FluminenseR. dos Trabalhadores, 420 - Vila Santa
*Volta Redonda**, Rio de Janeiro, Brasil*
*CEP 27255-125*
*Tel: +55-24-2107-3777*

2017-09-05 17:24 GMT-03:00 soumadwip ghosh <soumadwipghosh at gmail.com>:

> Hi,
> I am not sure why you used the gmx solvate command for putting the
> anionic species in your simulation box. It is meant for filling up the
> simulation box with water molceules as the resname 'SOL' in the
> topol.top file. Thus when you hit grompp it expects 'SOL' entry in
> your topology file, cant find it and prints an error. In my opinion,
> one should use the same gmx insert-molecules command for inserting the
> anionic part into the box. If you dont want to use water in the
> simulation you can proceed without the solvation step but cant use gmx
> solvate for inserting anionic species or anything else.
> Best
> Soumadwip Ghosh
> Post Doctoral Research Associate
> City of Hope Cancer Research Center
> Duarte 91010 CA
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