[gmx-users] different sets of fudgeQQ and fudgeLJ

Justin A. Lemkul jalemkul at vt.edu
Sun Sep 18 19:06:56 CEST 2011

Yun Shi wrote:
> Hi Mark,
> I don't quite understand what it follows "only one [defaults] section 
> can exist in an entire topology".
> Then how to specify different fudge values for different subsets of 
> non-bonded interactions?
> When defining new atom types, should I always use 'new' atomtypes names? 
> For example, if the atom type "H2" already exists for part A, then I 
> should use something different like "H2B" to define similar atomtypes in 
> part B?
> But if I can use only one [ defaults ] section, even within different 
> .itp files under the same .top file, how could I tell the program to 
> apply different fudge values to H2 as defined in A.itp and H2B as 
> defined in B.itp?

The values of fudgeLJ and fudgeQQ are applied to intramolecular 1-4 
interactions, thus they can only be present once in an entire topology.  They 
are global settings.  If you wish to define different 1-4 interactions, then 
define special [pairs], and if you want to use non-default nonbonded 
interactions, then define them in [nonbond_params].  The latter sounds like what 
you want, since it sounds like you want modified intermolecular interactions.


> Thanks,
> Yun
> Date: Sun, 18 Sep 2011 09:25:38 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>>
> Subject: Re: [gmx-users] different sets of fudgeQQ and fudgeLJ
> To: Discussion list for GROMACS users <gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <4E752C72.4040807 at anu.edu.au 
> <mailto:4E752C72.4040807 at anu.edu.au>>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 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
>  >       0.8333
>  >
>  > 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.
> Mark


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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