[gmx-users] Simulation of nonaqueous solvents

Tue Jan 5 19:33:31 CET 2016

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
>>>>
>>>> * Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>> posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>>
>>>
>>>
>>> --
>>> Diana Lousa
>>> Post-doc
>>> Protein Modeling Laboratory
>>> ITQB/UNL
>>> Oeiras, Portugal
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>
>>
>>
>> --
>> || radhe radhe ||
>>
>> abhishek
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
>

-- 
==================================================

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

==================================================