[gmx-users] Molecular Simulation using Ionic liquid

[Vidya Sundaram]

Hi,

I intend to simulate a protein of interest in the ionic liquid,1-Butyl-3-
methylimidazolium chloride (BmimCl). In order to generate the topology and
coordinate files of the IL, I tried optimizing the structure through
Gaussian09. Kindly clarify my doubts regarding the same.

1. Should the cation and anion structures be generated separately in
vacuum? or should it be generated by using water as solvent?

2. If it is to be generated in solvation model, I guess Gaussian needs
solvent descriptors (eps, epsinf and hydrogen bond acidity etc to be
specified when using SCF=SMD and Solvent= Generic). In that case, how do I
give these solvent descriptors separately for anion and cation?

Any information could really help.

Thanks in advance.

Vidya