[gmx-users] Simulation of nonaqueous solvents

[Mark Abraham]

Hi,

On Mon, Jan 4, 2016 at 6:57 PM abhishek khetan <askhetan at gmail.com> wrote:

> Is there a procedure/tutorial/method to calculate ssimulate ions in
> non-aqueous solvents from scratch?


The general advice is here
http://www.gromacs.org/Documentation/How-tos/Parameterization, but for
relatively common species, you might get lucky and find a publication (or
the GROMACS contribution section) that has what you need. Trust, but verify.


> 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.


Sure. The parameters are not magic - they are expensive to compute and
verify and people have only done the work for the combinations they want to
use.


> 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:
>
> $ 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.
>

The OPLS-AA in GROMACS has DMSO defined, but pdb2gmx can't help you if you
name it LIG in your .gro file. Name it DMSO (but don't break the column
requirements of the file format).

Mark


> 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
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