[gmx-users] Ryckaert-Bellemans again

[Anton Feenstra]

A. und B. Nick wrote:
> Dear Anton, 
> 
>>>I want to use the RB potential for simulation 
>>>of a amorphous PE box containing 20 chains. 
>>>To this I changed the dihedral type to "3". 
>>>How can I make sure that the 1,4 interactions 
>>>are removed? 
>>>If I used pdb2gmx to generate the topology file 
>>>I allways get a [pairs] section. Do I have 
>>>to delete this manually? 
>>
> 
>>You'll have to add a pair definition for each 1-4 interaction 
>>that you want removed. If you used pdb2gmx, they should already 
>>be there, so I don't see that you would need to add or remove 
>>anything manually. Simply changing dihedral type should work. 
>>-- 
>>Groetjes, 
>>Anton 
> 
> 
> Indeed I have the pair definition in my topol_?.itp files.
> But, if the 1,4 interactions are removed in this way,
> why do I see a LJ-14 energy term in the md.log
> file as well as the g_energy program. Shouldn't this
> contribution be zero if I exclude the 1,4 interactions
> with the RB potential?

defining a [ pairs ] interaction changes the corresponding
iteraction from a regular LJ to a LJ-14. It does not directly
remove the iteraction. For that, you might want to explicitly
put them in the [ exclusions ], but that also takes the Coulomb
interaction away. the [ pairtypes ] (e.g. in ff*bon.itp files)
defines the parameters for the LJ-14 interactions.

> And why do I need a [pairtypes] entry for my CH2 
> atom type in the ffgmxnb.itp file to run grompp successfully?
> I guessed that this is not needed if 1,4 interactions are 
> excluded.

Indeed, see above.


-- 
Groetjes,

Anton
  ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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