[gmx-users] OPLSAA parameters
Mark.Abraham at anu.edu.au
Fri Nov 21 07:54:23 CET 2008
> So to obtain the parameters(e.g. bonds) in topology file,
> 1, read bond atoms in .top (e.g. 1 2)
> 2, find atom types of the bond atoms in .top (e.g. oplsaa_235,
> 3, find atom names of the above atom types in ffoplsaanb.itp (e.g. C, O)
> 4, check parameters in ffoplsaabon.itp
> Is that right?
3 is irrelevant. Otherwise, you're on track. The general idea is that
indices in [bonds] look up the atom indices in [atoms] to get the atom
types which are looked up in [bondtypes] to get the parameters which are
then applied to the bonds.
> why it comes to such complex in GMX?
I think it's about as simple as it can be to do all the jobs it needs to
do. You need a central repository of parameters. You need a list of
bonds, and a way to map bonded atoms to parameters. You need a mechanism
that can span multiple force field designs.
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