[gmx-users] Molecular Simulation using Ionic liquid
baptista at itqb.unl.pt
Tue Jul 25 21:23:48 CEST 2017
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:
And its use with a protein: http://dx.doi.org/10.1021/jp0766050
On Tue, 25 Jul 2017, Mark Abraham wrote:
> 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:
>> 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.
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