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