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

Lee Soin nomadoro at gmail.com
Mon Jul 27 17:42:48 CEST 2009

So there is no place to specify electrostatic interactions for pair

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

> 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.
> Mark
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Department of Physics
Nanjing University, China
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