[gmx-users] OPLSAA parameters

[Mark Abraham]

friendli wrote:
> 
> 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, 
> oplsaa_236)
> 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.

Mark