[gmx-users] Ryckaert-Bellemans again

A. und B. Nick ANick at t-online.de
Fri Jan 24 15:36:00 CET 2003

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. 

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?

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 


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