[gmx-users] (no subject)
cmb411 at psu.edu
Tue Oct 21 00:10:01 CEST 2003
On Sun, 19 Oct 2003 21:37:11, Erik Lindahl wrote:
> Hi Corina,
> There are a couple of steps:
> 1. Find out exactly what the interaction forms are for bonds, angles,
> proper dihedrals (sometimes called torsions), and improper or
> out-of-plane torsions/dihedrals. If we can represent these, we're set,
> but in some cases we have to take a factor 2 into account. If not, it
> depends on the type of interaction you need. For instance: using a new
> type for bonded interactions isn't too difficult (see e.g. how we use
> both standard and Gromos96 bonds), but having nonbonded interactions
> between triplets of atoms would be very difficult to do...
> 2. Check how the force fields use atom types. Does each atom type
> correspond to unique bonded and nonbonded parameters (like Gromos96 &
> Amber), or is it like OPLS, where there are more nonbonded than bonded
> 3. Implement the atom types in ffXXX.atp (easy), and add the nonbonded
> parameters to ffXXXnb.itp. Most forcefields use combination rules and a
> small number of atom types, but Gromacs can handle different parameters
> for every single pair of atoms. You will need to check whether your
> force field uses c6/c12 or sigma/epsilon parameters. Some
> implementations don't specify sigma, but the minimum radius - that's
> easy to convert, though.
> 4. Implement the parameters for bonds, angles and dihedrals in
> ffXXXbon.itp. This can be complicated if your forcefield has thousands
> of atom types like OPLS, but in most cases it's easy.
> 5. At this point you have a finished force field. To build topologies
> automatically you also want to implement the building blocks in
> ffXXX.rtp, but don't write it from scratch - just pick one of the
> existing force fields and edit that.
> On Sunday, October 19, 2003, at 02:54 PM, CORINA BARBU wrote:
> > Hello!
> > I need to use a different force field (MM2/MM3) from those already
> > implemented
> > in GROMACS. I wonder how difficult is to implement it. At the first
> > sight it
> > seems to me that I need to provide an *.itp file (ff--bon.itp,
> > ff--nb.itp,
> > ff--.atp) for my case, with parameters taken from literature. I would
> > also have
> > to indicate what terms to consider in the expresion of the energy
> > functional.
> > And this can be indicated in the column 'func' in the *.itp file
> > containing the
> > definition of the molecule. If GROMACS already has the
> > interaction-functions
> > that I need, then I just need to choose some of them. If not, I have
> > to code
> > what doesn't exist.
> > I'm interested in the coding part...what would I need to code for a
> > new force
> > field?
> > Thanks very much! Corina
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