[gmx-users] different sets of fudgeQQ and fudgeLJ

Yun Shi yunshi09 at gmail.com
Sun Sep 18 19:02:34 CEST 2011

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


Date: Sun, 18 Sep 2011 09:25:38 +1000
From: Mark Abraham <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>
Message-ID: <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.

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