[gmx-users] Molecular Simulation using Ionic liquid

Mark Abraham mark.j.abraham at gmail.com
Tue Jul 25 19:23:32 CEST 2017


How have others done similar work? Hint: extending a protein forcefield
means understanding how its parameters were developed. You can't just
assume that your favourite tool is the one for the job.


On Tue, 25 Jul 2017 08:37 Vidya Sundaram <vidya.sundaram86 at gmail.com> wrote:

> 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
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