[gmx-users] LJ parameters

[Erik Lindahl]

Pedro Alexandre de Araujo Gomes Lapido Loureiro wrote:

>>>Hello,
>>>
>>>I wish to simulate a DPPC bilayer, using the GROMOS96 45a3 LJ parameters for
>>>
>>>the
>>>CH2/CH3 of the lipid tails (CL2/CL3).
>>>
>>Be warned that Alex de Vries in Groningen has tested this, and the 
>>Gromos96 force field
>>still results in much too low areas/lipid, even with the new tail 
>>parameters.
>>
>
>Yes, I know that :( , but I am using non-zero surface-tension to "circumvent" 
>this weakness in the forcefield.
>
>
>>1. If an interaction is given explicitly in the [ pairs ] (1,4) or [ 
>>nonbond_params ] (normal interactions),
>>    that value will always be used.
>>
>Even if I say "generate pairs=yes" bearing in mind those pairs not included in 
>the [pairs] section?
>

Yes, the explicitly listed interactions override the generated ones. 
Just comment out the ones
you don't want if that's a problem.

Cheers,

Erik