[gmx-developers] add ECEPP3 to gromacs
feenstra at few.vu.nl
Mon May 8 20:41:04 CEST 2006
Mark Abraham wrote:
> Compare the parameters in the already-implemented force fields to the
> values for those parameters in the literature to confirm you understand
> everything properly.
First, if you haven't already, make sure you RTFM (Read The Fine
Manual). That's what it's for! There is a reasonably excellent chapter
on forcefields and another on topology files, most of which also applies
to the forcefield files.
The differences you note for OPLS versus Amber forcefields, derive from
the (slightly) different phylosophy these ff's seem to follow. In OPLS
mass is thought to be a property of the atom, and a default charge is
given as well for each atom type. In Amber, however, charge is thought
to be a property of the molecule (or building block), and for some
reason, mass is included there as well. So, in order to keep as close as
possible to the way these forcefields were designed and implemented
originally, they are included differently in Gromacs.
For your ECEPP3 ff, you should choose whichever method fits best to the
design of that ff. I think (but I'm not sure), you could also use
explicit mass with charges 0 in the ff*nb.itp file and only assign
charges in the .rtp (you wouldn't normally want a building block with a
different mass for a certain atom type).
Finally, technically, the ff*.itp files define the forcefield proper
(i.e., all the forcefield parameters, e.g. charge, bond length, dihedral
strength, etc.), while the ff*.rtp file specifies the building block.
Unfortunately, the rtp file also will contain forcefield-specific
information (out of necessity in the current implementation), like the
mapping of atom types to specific atoms in the building blocks, and
bonded interaction types to bonds, angles, etc.
* NOTE: New Affiliation, Phone & Fax numbers (below) *
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| _ _ ___,| K. Anton Feenstra |
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| | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" (RHCP) |
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