[gmx-users] Simulation of nonaqueous solvents

Tue Jan 5 20:01:50 CET 2016

i checked out all the suggestions
1) the oplsaa topology and forcefields are available in for all the
solvents that i wanted from http://virtualchemistry.org .
2) The database in share/gromacs/top does contain some solvents and ions
too but mostly for only the cations. Cl- was the lone anion.
3) As it seems, anions are the only thing I'm missing. Although I do not
know how they have gotten the FF parameters and topologies for so many
anions http://pubs.acs.org/doi/abs/10.1021/jacs.5b01004 . In the SI, all
they show is their calculated results against the experimental ones. They
do not tell how they get the FF and topology files. I should probably shoot
them an email.

Thanks for all your replies.
Best

On Tue, Jan 5, 2016 at 7:33 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/5/16 1:30 PM, Diana Lousa wrote:
>
>> Hi,
>> Probably it will be difficult to find the parameters for all the molecules
>> that you want to simulate in any given FF and you are right that you
>> should
>> be consistent and use parameters derived in the scope of the same FF.
>> Deriving parameters is indeed a difficult task and as far as I know good
>> parameters for ions are hard to get and I cannot help with that because I
>> have never done it.
>> Gromacs implements several FF that are included in the gromacs package.
>> You
>> can go to the directory where you have installed gromacs and you should
>> find a directory called share/top. Inside that directory you have the
>> files
>> for the different FF and there you can check which molecules are available
>> in each FF. This is probably what you mean by "gromacs database".  But you
>> should be careful and check where these parameters come from, i.e., read
>> the original papers.
>>
>>
> The anions are a challenge.  The cations and most (if not all) of the
> proposed solvents exist in, e.g. CHARMM and perhaps other force fields.  At
> minimum, they are easily built from existing groups.  The anions may not be
> straightforward, based on chemical coverage of any force field.
> Polarization effects could be significant in some of them, too, which
> requires the use of entirely different models...
>
> -Justin
>
>
> Best
>>
>> Diana
>>
>> On Tue, Jan 5, 2016 at 2:09 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
>>>>>
>>>>> --
>>>>> Gromacs Users mailing list
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>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Diana Lousa
>>>> Post-doc
>>>> Protein Modeling Laboratory
>>>> ITQB/UNL
>>>> Oeiras, Portugal
>>>> --
>>>> Gromacs Users mailing list
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>>>>
>>>
>>>
>>> --
>>> || radhe radhe ||
>>>
>>> abhishek
>>> --
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>>
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
|| radhe radhe ||

abhishek