[gmx-users] OPLSAA parameters

friendli friendli2000 at gmail.com
Fri Nov 21 08:35:58 CET 2008

Hi Mark,

the atom types in .top file is opls_???, but the atom types(or "name") 
in [bondtypes] in ffoplsaabon.itp file is C, H, CT, C_3, etc.

So we still need to look up ffoplsaanb.itp to link these two "atom type" 
(or "name"), right?



Mark Abraham wrote:
> 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
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