[gmx-users] Non-biomolecular systems on Gromacs: incorporating a force field
lindahl at cbr.su.se
Mon Oct 16 21:41:29 CEST 2006
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
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
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.
On Oct 11, 2006, at 9:30 PM, Marin Djendjinovic wrote:
> 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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