[gmx-users] Simulation of nonaqueous solvents

[Diana Lousa]

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