[gmx-users] About exclusion of non-bonded interaction for pairs of energy groups
nomadoro at gmail.com
Mon Jul 27 15:56:08 CEST 2009
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
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
>> the parameters for OPLS in the .itp files are specified for each atom, so
>> 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.
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Department of Physics
Nanjing University, China
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