[gmx-users] Molecular Simulation using Ionic liquid

[Antonio Baptista]

Hi Vidya,

You should try to make your model "fit" into the existing forcefield you 
will be using. Also, you should validate the model with known physical 
properties (e.g., density, self-diffusion, shear viscosity, isothermal 
compressibility). It's usually difficult to get them all good, of course, 
but playing with some (e.g., LJ) parameters may get you a reasonable 
compromise. An example of a parameterization of Bmim for a GROMOS ff: 
http://dx.doi.org/10.1021/jp061869s
And its use with a protein: http://dx.doi.org/10.1021/jp0766050

Best,
Antonio


On Tue, 25 Jul 2017, Mark Abraham wrote:

> Hi,
>
> 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.
>
> Mark
>
> 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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