[gmx-users] Simulation of nonaqueous solvents

[abhishek khetan]

Okay, I will try to broadly explain what i want to do and what i need. As
mentioned earlier, it would be amazing if you could direct me to some
sources with these methods. I am more than 100% sure there are many liek me
who will benefit from such a technique.

What I want to do is study ion-pair formation in several different non
aqueous solvents. Here the ion pairs are essentially cations like
Li+/Na+/K+/NH4+ paired with anions like TFSI-/NO3-/PF6-/ClO4-/O2-. I want
to study their pairing in different solvents which are dimethoxyethane (or
simply glyme), dimethylsulfoxide, acetonitrile and if possible also in
tetrahydrofuran, dimethyacetamide, dimethylformamide. My aim is to
eventually look at the solvation shell and the solvation energetics using a
QM/MM approach in Gaussian. However, before that I would like 1) do the MD
simulations and see what i can learn about my systems, ion-pairing and
calculate diffusivity and viscosity of these solutions and 2) to make sure
that I really need the QM/MM approach at all.

For making a comparative study I'll need to be totally consistent with my
choice of the force field. Searching for the values for what i need - I did
exactly that before requesting for a method here. However, 1) not all the
data is available for making a comparative study that I want to do, 2) the
available data/parameters are often across force fields, in fact mostly
belonging to different force fields, which defeats the purpose.

Thats why I was wondering if I could get the parameters for all these
species in a consistent way for any one forcefield. Taking a look at the
page http://www.gromacs.org/Documentation/How-tos/Parameterization is kind
of discouraging as it has been repeated many times that this is not an easy
task. Its okay if it takes some time but what I want to be sure about that
its possible in the end and there is a consisten way to do it.

apart from this, could you please point me to a list of what all cations/
anions / and nonaqueous electrolytes are already in the gromacs database ?
>From what I have mentioned, it seems that a lot of species should already
be there.

thanks for your patient perusal


On Tue, Jan 5, 2016 at 11:56 AM, Diana Lousa <dlousa at itqb.unl.pt> wrote:

> Hi,
> I am not completely sure of what you intend to do, i.e. do you want to
> simulate just the ions in solution or do you want to study protein-ion
> interactions in nonaqueous solvents? The latter issue has been addressed by
> us in this work http://pubs.acs.org/doi/abs/10.1021/jp303008g. You can
> find
> Lennard Jones parameters for  alakali and halide ions here
> http://scitation.aip.org/content/aip/journal/jcp/134/14/10.1063/1.3567022.
> Regarding nonaqueous solvents, you should search for parameters for the
> solvents of interest in the literature and then make sure these parameters
> are reliable (i.e. check if they reproduce the experimental
> physical-chemical properties of the solvent). Some solvent and ion
> parameters are already available with standard FF such a GROMOS 54a7.
>
> Diana
>
> On Mon, Jan 4, 2016 at 7:09 PM, David van der Spoel <spoel at xray.bmc.uu.se>
> wrote:
>
> > On 04/01/16 18:56, abhishek khetan wrote:
> >
> >> Is there a procedure/tutorial/method to calculate ssimulate ions in
> >> non-aqueous solvents from scratch? By "scratch" I mean that the the
> >> solvents I am trying to use (like dimethylsulfoxide or tetrahydrofuran
> or
> >> acetonitrile) and the ions ( Li+, Na+, etc )are way simpler than the
> huge
> >> protiens people usually solvate in water, but these species dont have
> >> entries in the database that gromacs uses. I face the problem that when
> I
> >> create a solvent box (dmso_box.gro, verified visually) and then try to
> >> generate its topology file by using the command:
> >>
> > Check our website
> > http://virtualchemistry.org
> > with validated topologies and coordinate files for about 150 liquids and
> > three force fields.
> >
> >>
> >> $ gmx_mpi pdb2gmx -f dmso_box.gro -o DMSO.gro
> >>
> >> Where in I interactively use the forcefield as 15 (OPLS-AA) and water
> as 7
> >> (none), I get the error:
> >>
> >> Residue 'LIG' not found in residue topology database.
> >>
> >> I am pretty sure that this must be possible by doing some other
> >> calculations, etc to get the required data for specifying bonds, angles,
> >> charges, their interaction parameters etc. Any help in this regard would
> >> be
> >> highly appreciated
> >>
> >> Best,
> >> Abhishek
> >>
> >>
> >
> > --
> > David van der Spoel, Ph.D., Professor of Biology
> > Dept. of Cell & Molec. Biol., Uppsala University.
> > Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> > spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
> >
> > --
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>
>
> --
> Diana Lousa
> Post-doc
> Protein Modeling Laboratory
> ITQB/UNL
> Oeiras, Portugal
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-- 
|| radhe radhe ||

abhishek