[gmx-users] Simulation of nonaqueous solvents

[abhishek khetan]

Sorry forgot to mention, I am totally new to gromacs, so i might not be
correct with some of the semantics.

On Tue, Jan 5, 2016 at 3:09 PM, abhishek khetan <askhetan at gmail.com> wrote:

> 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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>> Gromacs Users mailing list
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>
>
>
> --
> || radhe radhe ||
>
> abhishek
>



-- 
|| radhe radhe ||

abhishek