[gmx-developers] add ECEPP3 to gromacs

Anton Feenstra 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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