[gmx-users] About exclusion of non-bonded interaction for pairs of energy groups

[Lee Soin]

I see in the .top file generated by pdb2gmx:
[ pairs ]
;  ai    aj funct            c0            c1            c2            c3

The [ pairs ] directive accepts these four parameters c0, c1, c2 and c3. Do
c2 and c3 parametrize electrostatic interactions? And what do they stand for
respectively? Thanks!


2009/7/27 Mark Abraham <Mark.Abraham at anu.edu.au>

> Lee Soin wrote:
>
>> My problem is actually as follows:
>>
>
> Please describe in as full detail as reasonable the first time :-)
>
>  I have three groups of atoms: A, B and C. Now I want to keep full
>> interaction between A-B and A-C, but only retain the repulsive part of VDW
>> interaction between B-C. I'm using the OPLS force field. It seems to me
>> that
>> the parameters for OPLS in the .itp files are specified for each atom, so
>> is
>> there any way to treat the interaction pairwise?
>>
>
> Yes, use [ pairs ] directives to overrride the atomtype-based lookup. That
> will be tedious if there are many such atoms. Read parts of chapter 5.
>
> Probably, no force field was parameterized to reproduce whatever it is
> you're trying to observe.
>
>
> Mark
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-- 
SUN Li
Department of Physics
Nanjing University, China
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