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

Mark Abraham Mark.Abraham at anu.edu.au
Mon Jul 27 17:10:53 CEST 2009

Lee Soin wrote:
> 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!

No, they're two pairs of VDW parameters, one pair each for two possible 
states for a free-energy calculation. The tables in chapter 5 imply 
this, but it is not at all obvious to a newcomer.

>> 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.

You should still do this.


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