[gmx-users] Simulation of nonaqueous solvents

[Justin Lemkul]

On 1/4/16 12:56 PM, 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:
>
> $ 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
>

Well, if you use the proper residue name (DMSO), then OPLS, all GROMOS variants, 
and our CHARMM36 support it.  Most small molecules like you've mentioned are 
indeed building blocks for biomolecular force fields, and should be present in 
the literature, at minimum.  The force field files in GROMACS tend to be 
protein- and nucleic acid-centric, but incorporating new molecules is 
straightforward.

-Justin

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

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

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