[gmx-users] different sets of fudgeQQ and fudgeLJ
Mark.Abraham at anu.edu.au
Sun Sep 18 01:25:38 CEST 2011
On 18/09/2011 8:58 AM, Yun Shi wrote:
> Hi all,
> I want to apply different values of LJ and QQ scaling factors for two
> interacting molecules A and B. Since I already have the .itp files for
> each molecule, should I just add something like:
> [ defaults ]
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> 1 2 yes 0.5
> at the very beginning of A.itp and B.itp respectively (the actual
> values are different from this eg.)?
> I wonder if .itp file format was designed for this kind of purpose?
> :) I guess we could even define different sets of atom types for A
> and B, right?
As you will see in the examples in chapter 5, only one [defaults]
section can exist in an entire topology. Further, the fudge values only
apply to a subset of non-bonded interactions. For the kind of
calculation you have in mind, you will need to define new atom types for
the modified interactions.
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