[gmx-users] Non-biomolecular systems on Gromacs: incorporating a force field

[Erik Lindahl]

Hi Marin,

That is probably quite straightforward. Biomolecular systems are  
special in that they have lots of (complicated) bonded interactions,  
and require somewhat elaborate rules to create topologies from amino  
acid building blocks.

For "simpler" systems it is often just a matter of skipping 90% of  
this and create a simple (manual) topology from scratch.

Why don't you start with a more detailed description of the systems  
you want to simulate? What atoms do you have? How are the parameter  
specified? What are the functional forms?

Gromacs uses the C preprocessor when reading topologies, so the  
actual force field files are #included in the top-level topology. The  
simplest (but not best) force field is "ffgmx", and the actual files  
locates in <gromacs dir>/share/top/.  _Very_ briefly:

A) The file ffXXX.itp includes (i) nonbonded interactions from  
ffXXXnb.itp and (ii) bonded interactions from ffXXXbon.itp
B) In ffXXXnb.itp, we first define atom types as well as van der  
Waals parameters.
      Some force fields (e.g. OPLS) then use combination rules for  
all cross-type interactions, while others (gmx) list specific  
parameters. Similarly, 1-4 bonded parameters can either be calculated  
by scaling or listed explicitly.
C) ffXXXbon.itp contains specifications for bonds, angles, and  
torsions for all atom types.

That is often all you need for the force field. There is another  
bunch of ffXXX.yyy files, but most of these are only used when  
building protein topologies automatically from PDB files.

You will still need to create a topology for your actual molecule.  
This is essentially a list of all atoms in a molecule, with charge,  
charge groups, mass, etc., followed by lists of bonds, angles, and  
torsions present (for proteins we create this automatically with  
pdb2gmx).

The easiest way to understand the topology file is probably to go  
through a couple of the tutorials and see what the .top files look  
like. All these formats are also specified in detail in the  
"Topology" section of the manual.

Cheers,

Erik


On Oct 11, 2006, at 9:30 PM, Marin Djendjinovic wrote:

> Hi,
>
> I have couple of newbie questions that I hope someone will have
> patience to answer.  I have some experience with MD
> simulation and none with Gromacs.
>
> I have been using Tinker package for about half a year, but I
> find it a little unfriendly (not a very thorough manual and it's
> written in Fortran which is not my cup of tea :))
>
> I see that most of tutorials and explanations on Gromacs site are
> related to proteins. Is there a reason Gromacs would not be a
> good choice for other systems, such as silica, for example?
>
> I would like to incorporate force field for silica in the
> Gromacs. Now where do I start? What source files would I need to
> modify? It's OK if you can't give me a detailed answer, but at least
> a starting point, a little bit more then that flow chart on the
> Gromacs website.
>
> Thanks for your help.
>
>
>
>
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