[gmx-users] New force fields
David L. Bostick
dbostick at physics.unc.edu
Thu May 2 23:49:55 CEST 2002
There are a few features used for amorphous materials that may prove to be
useful to some...
valence angle potentials:
van der Waals potentials:
n - m potential
Shifted n - m potential
et al.. you can see the DL_POLY_2 Reference Manual (CCP5 website) for more
details on these if they are of interest. Also since everyone is talking
about implementing other forcefields it should be noted that 1-4
interactions can be a real headache. With current gromacs/gromos
parameters, it is customary to have no charge-charge fudge factor, but for
OPLS 1-4 LJ is
scaled by 1/8 and charge-charge interactions are scaled by 1/2 .. or the
other way around. For standard amber (all-atom) it is different. This
becomes hectic if you have molecular species where some things need to be
screened and others don't.. i.e. ryckaert bellemans tails on lipids with
OPLS parameters, since there is only 1 place to put a fudgeQQ factor in
gromacs... or rather, when some species must be screened differently than
others. DL_POLY handles this by placing individual screening factors to be
read into the program in the same place that dihedrals are read in. THis
way each dihedral can have a different 1-4 interaction in the system..
Currently such problems can be dealt with for LJ interactions by using a
simple pairlist and having [pairtypes] tags in the topology files, but for
1-4 charge-charge interactions, nothing like this can be dealt with.
I'm not saying these are all things to worry about.. but just food for
David Bostick Office: 262 Venable Hall
Dept. of Physics and Astronomy Phone: (919)962-0165
Program in Molecular and Cellular Biophysics
CB #3255 Phillips Hall dbostick at physics.unc.edu
Chapel Hill, NC 27599 http://www.unc.edu/~dbostick
On Thu, 2 May 2002, Erik Lindahl wrote:
> We should have AMBER, CHARMM& OPLS working relatively soon, but since
> we're anyway moving to the new XML formats in the next version it might
> be smart to think if there are additional strange parameter formats or
> forcefields with strange interactions, so we can prepare the force field
> descriptions for this.
> There are a couple of things I've thought about, but I'd be happy for
> more suggestions. We should try to add support for:
> 1. Separate bonded and nonbonded atom types. This is already done - it's
> quite useful for OPLS with 965 different nonbonded atom types.
> (965^4=8.7e11 dihedral definitions is a little unnecessary...)
> 2. Proper & improper dihedral definitions that use either 4 or 2 atoms.
> Wildcards should also be ok in all interactions. This is essentially
> finished too.
> 3. Automated generation of 1-3 (Urey-Bradley) interactions. These can be
> defined as pairs now, but it should be cleaner & automatic.
> Are there other features used by some force fields? Some ancient
> versions of AMBER used to need 10-12 interactions, but I don't think
> anybody is using it now...
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